wwpdb

Main Index

ANISOU

TER

HETATM

ENDMDL

Coordinate Section

The Coordinate Section contains the collection of atomic coordinates as well as the MODEL and ENDMDL records.

MODEL

Overview

The MODEL record specifies the model serial number when multiple models of the same structure are presented in a single coordinate entry, as is often the case with structures determined by NMR.

Record Format

COLUMNS    DATA TYPE  FIELD     DEFINITION
---------------------------------------------------------------------------------------
 1 - 6    Record name  "MODEL "
11 - 14    Integer    serial     Model serial number.

Details

This record is used only when more than one model appears in an entry. Generally, it is employed mainly for NMR structures. The chemical connectivity should be the same for each model. ATOM, HETATM, ANISOU, and TER records for each model structure and are interspersed as needed between MODEL and ENDMDL records.
The numbering of models is sequential, beginning with 1.
All models in a deposition should be superimposed in an appropriate author determined manner and only one superposition method should be used. Structures from different experiments, or different domains of a structure should not be superimposed and deposited as models of a deposition.
All models in an NMR ensemble should be homogeneous – each model should have the exact same atoms (hydrogen and heavy atoms), sequence and chemistry.
All models in an NMR entry should have hydrogen atoms.
Deposition of minimized average structure must be accompanied with ensemble and must be homogeneous with ensemble.
A model cannot have more than 99,999 atoms. Where the entry does not contain an ensemble of models, then the entry cannot have more than 99,999 atoms. Entries that go beyond this atom limit must be split into multiple entries, each containing no more than the limits specified above.

Verification/Validation/Value Authority Control

Entries with multiple models in the NUMMDL record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models.

Relationships to Other Record Types

Each MODEL must have a corresponding ENDMDL record.

Examples

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL    1
ATOM   1 N  ALA A  1   11.104  6.134 -6.504 1.00 0.00      N
ATOM   2 CA ALA A  1   11.639  6.071 -5.147 1.00 0.00      C
... ...
... ...
... ...
ATOM  293 1HG GLU A 18  -14.861 -4.847  0.361 1.00 0.00      H
ATOM  294 2HG GLU A 18  -13.518 -3.769  0.084 1.00 0.00      H
TER   295   GLU A 18                      
ENDMDL                               
MODEL    2                            
ATOM  296 N  ALA A  1   10.883  6.779 -6.464 1.00 0.00     N
ATOM  297 CA ALA A  1   11.451  6.531 -5.142 1.00 0.00     C
... ...
... ...
ATOM  588 1HG GLU A 18  -13.363 -4.163 -2.372 1.00 0.00     H
ATOM  589 2HG GLU A 18  -12.634 -3.023 -3.475 1.00 0.00     H
TER   590   GLU A 18                     
 ENDMDL

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
MODEL    1
ATOM   1 N AALA A  1   72.883 57.697 56.410 0.50 83.80      N 
ATOM   2 CA AALA A  1   73.796 56.531 56.644 0.50 84.78      C 
ATOM   3 C AALA A  1   74.549 56.551 57.997 0.50 85.05      C 
ATOM   4 O AALA A  1   73.951 56.413 59.075 0.50 84.77      O 
...
...
...
HETATM37900 O AHOH  490   -24.915 147.513 36.413 0.50 41.86      O 
HETATM37901 O AHOH  491   -28.699 130.471 22.248 0.50 36.06      O 
HETATM37902 O AHOH  492   -33.309 184.488 26.176 0.50 15.00      O 
ENDMDL                                     
MODEL    2                                 
ATOM   1 N BALA A  1   72.883 57.697 56.410 0.50 83.80      N 
ATOM   2 CA BALA A  1   73.796 56.531 56.644 0.50 84.78      C 
ATOM   3 C BALA A  1   74.549 56.551 57.997 0.50 85.05      C 
ATOM   4 O BALA A  1   73.951 56.413 59.075 0.50 84.77      O 
ATOM   5 CB BALA A  1   74.804 56.369 55.453 0.50 84.29      C 
ATOM   6 N BASP A  2   75.872 56.703 57.905 0.50 85.59      N 
ATOM   7 CA BASP A  2   76.801 56.651 59.048 0.50 85.67      C 
ATOM   8 C BASP A  2   76.283 57.361 60.309 0.50 84.80      C 
...

The ATOM records present the atomic coordinates for standard amino acids and nucleotides. They also present the occupancy and temperature factor for each atom. Non-polymer chemical coordinates use the HETATM record type. The element symbol is always present on each ATOM record; charge is optional.

Changes in ATOM/HETATM records result from the standardization atom and residue nomenclature. This nomenclature is described in the Chemical Component Dictionary (https://files.wwpdb.org/pub/pdb/data/monomers).

Record Format

COLUMNS    DATA TYPE  FIELD    DEFINITION
-------------------------------------------------------------------------------------
 1 - 6    Record name  "ATOM "
 7 - 11    Integer    serial    Atom serial number.
13 - 16    Atom     name     Atom name.
17       Character   altLoc    Alternate location indicator.
18 - 20    Residue name resName   Residue name.
22       Character   chainID   Chain identifier.
23 - 26    Integer    resSeq    Residue sequence number.
27       AChar     iCode    Code for insertion of residues.
31 - 38    Real(8.3)   x      Orthogonal coordinates for X in Angstroms.
39 - 46    Real(8.3)   y      Orthogonal coordinates for Y in Angstroms.
47 - 54    Real(8.3)   z      Orthogonal coordinates for Z in Angstroms.
55 - 60    Real(6.2)  occupancy  Occupancy.
61 - 66    Real(6.2)  tempFactor  Temperature factor.
77 - 78    LString(2)  element   Element symbol, right-justified.
79 - 80    LString(2)  charge    Charge on the atom.

Details

ATOM records for proteins are listed from amino to carboxyl terminus.
Nucleic acid residues are listed from the 5' to the 3' terminus.
Alignment of one-letter atom name such as C starts at column 14, while two-letter atom name such as FE starts at column 13.
Atom nomenclature begins with atom type.
No ordering is specified for polysaccharides.
Non-blank alphanumerical character is used for chain identifier.
The list of ATOM records in a chain is terminated by a TER record.
If more than one model is present in the entry, each model is delimited by MODEL and ENDMDL records.
AltLoc is the place holder to indicate alternate conformation. The alternate conformation can be in the entire polymer chain, or several residues or partial residue (several atoms within one residue). If an atom is provided in more than one position, then a non-blank alternate location indicator must be used for each of the atomic positions. Within a residue, all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator. There are two ways of representing alternate conformation- either at atom level or at residue level (see examples).
For atoms that are in alternate sites indicated by the alternate site indicator, sorting of atoms in the ATOM/HETATM list uses the following general rules:

- In the simple case that involves a few atoms or a few residues with alternate sites, 
 the coordinates occur one after the other in the entry.
- In the case of a large heterogen groups which are disordered, the atoms for each conformer 
 are listed together.

Alphabet letters are commonly used for insertion code. The insertion code is used when two residues have the same numbering. The combination of residue numbering and insertion code defines the unique residue.
If the depositor provides the data, then the isotropic B value is given for the temperature factor.
If there are neither isotropic B values from the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.
Columns 79 - 80 indicate any charge on the atom, e.g., 2+, 1-. In most cases, these are blank.
For refinements with program REFMAC prior 5.5.0042 which use TLS refinement, the values of B may include only the TLS contribution to the isotropic temperature factor rather than the full isotropic value.

Verification/Validation/Value Authority Control

The ATOM/HETATM records are checked for PDB file format, sequence information, and packing.

Relationships to Other Record Types

The ATOM records are compared to the corresponding sequence database. Sequence discrepancies appear in the SEQADV record. Missing atoms are annotated in the remarks. HETATM records are formatted in the same way as ATOM records. The sequence implied by ATOM records must be identical to that given in SEQRES, with the exception that residues that have no coordinates, e.g., due to disorder, must appear in SEQRES.

Example

 1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 32 N AARG A -3 11.281 86.699 94.383 0.50 35.88 N 
ATOM 33 N BARG A -3 11.296 86.721 94.521 0.50 35.60 N
ATOM 34 CA AARG A -3 12.353 85.696 94.456 0.50 36.67 C
ATOM 35 CA BARG A -3 12.333 85.862 95.041 0.50 36.42 C
ATOM 36 C AARG A -3 13.559 86.257 95.222 0.50 37.37 C
ATOM 37 C BARG A -3 12.759 86.530 96.365 0.50 36.39 C
ATOM 38 O AARG A -3 13.753 87.471 95.270 0.50 37.74 O
ATOM 39 O BARG A -3 12.924 87.757 96.420 0.50 37.26 O
ATOM 40 CB AARG A -3 12.774 85.306 93.039 0.50 37.25 C
ATOM 41 CB BARG A -3 13.428 85.746 93.980 0.50 36.60 C
ATOM 42 CG AARG A -3 11.754 84.432 92.321 0.50 38.44 C
ATOM 43 CG BARG A -3 12.866 85.172 92.651 0.50 37.31 C
ATOM 44 CD AARG A -3 11.698 84.678 90.815 0.50 38.51 C
ATOM 45 CD BARG A -3 13.374 85.886 91.406 0.50 37.66 C
ATOM 46 NE AARG A -3 12.984 84.447 90.163 0.50 39.94 N
ATOM 47 NE BARG A -3 12.644 85.487 90.195 0.50 38.24 N
ATOM 48 CZ AARG A -3 13.202 84.534 88.850 0.50 40.03 C
ATOM 49 CZ BARG A -3 13.114 85.582 88.947 0.50 39.55 C
ATOM 50 NH1AARG A -3 12.218 84.840 88.007 0.50 40.76 N
ATOM 51 NH1BARG A -3 14.338 86.056 88.706 0.50 40.23 N
ATOM 52 NH2AARG A -3 14.421 84.308 88.373 0.50 40.45 N

 1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 32 N AARG A -3 11.281 86.699 94.383 0.50 35.88 N 
ATOM 33 CA AARG A -3 12.353 85.696 94.456 0.50 36.67 C
ATOM 34 C AARG A -3 13.559 86.257 95.222 0.50 37.37 C
ATOM 35 O AARG A -3 13.753 87.471 95.270 0.50 37.74 O
ATOM 36 CB AARG A -3 12.774 85.306 93.039 0.50 37.25 C
ATOM 37 CG AARG A -3 11.754 84.432 92.321 0.50 38.44 C
ATOM 38 CD AARG A -3 11.698 84.678 90.815 0.50 38.51 C
ATOM 39 NE AARG A -3 12.984 84.447 90.163 0.50 39.94 N
ATOM 40 CZ AARG A -3 13.202 84.534 88.850 0.50 40.03 C
ATOM 41 NH1AARG A -3 12.218 84.840 88.007 0.50 40.76 N
ATOM 42 NH2AARG A -3 14.421 84.308 88.373 0.50 40.45 N
ATOM 43 N BARG A -3 11.296 86.721 94.521 0.50 35.60 N
ATOM 44 CA BARG A -3 12.333 85.862 95.041 0.50 36.42 C
ATOM 45 C BARG A -3 12.759 86.530 96.365 0.50 36.39 C
ATOM 46 O BARG A -3 12.924 87.757 96.420 0.50 37.26 O
ATOM 47 CB BARG A -3 13.428 85.746 93.980 0.50 36.60 C
ATOM 48 CG BARG A -3 12.866 85.172 92.651 0.50 37.31 C
ATOM 49 CD BARG A -3 13.374 85.886 91.406 0.50 37.66 C
ATOM 50 NE BARG A -3 12.644 85.487 90.195 0.50 38.24 N
ATOM 51 CZ BARG A -3 13.114 85.582 88.947 0.50 39.55 C
ATOM 52 NH1BARG A -3 14.338 86.056 88.706 0.50 40.23 N

ANISOU

Overview

The ANISOU records present the anisotropic temperature factors.

Record Format

COLUMNS    DATA TYPE  FIELD     DEFINITION
-----------------------------------------------------------------
 1 - 6    Record name  "ANISOU"
 7 - 11    Integer    serial     Atom serial number.
13 - 16    Atom     name      Atom name.
17      Character   altLoc     Alternate location indicator
18 - 20    Residue name resName    Residue name.
22      Character   chainID    Chain identifier.
23 - 26    Integer    resSeq     Residue sequence number.
27      AChar     iCode     Insertion code.
29 - 35    Integer    u[0][0]    U(1,1)
36 - 42    Integer    u[1][1]    U(2,2)
43 - 49    Integer    u[2][2]    U(3,3)
50 - 56    Integer    u[0][1]    U(1,2)
57 - 63    Integer    u[0][2]    U(1,3)
64 - 70    Integer    u[1][2]    U(2,3)
77 - 78    LString(2)  element    Element symbol, right-justified.
79 - 80    LString(2)  charge     Charge on the atom.

Details

Columns 7 - 27 and 73 - 80 are identical to the corresponding ATOM/HETATM record.
The anisotropic temperature factors (columns 29 - 70) are scaled by a factor of 10**4 (Angstroms**2) and are presented as integers.
The anisotropic temperature factors are stored in the same coordinate frame as the atomic coordinate records.
ANISOU values are listed only if they have been provided by the depositor.

Verification/Validation/Value Authority Control

The depositor provides ANISOU records, and the wwPDB verifies their format.

Relationships to Other Record Types

The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic temperature factors as ,B(eq), as described in the ATOM and HETATM sections.

Example

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM  107 N  GLY A 13   12.681 37.302 -25.211 1.000 15.56      N
ANISOU 107 N  GLY A 13   2406  1892  1614  198  519  -328    N
ATOM  108 CA GLY A 13   11.982 37.996 -26.241 1.000 16.92      C
ANISOU 108 CA GLY A 13   2748  2004  1679  -21  155  -419    C
ATOM  109 C  GLY A 13   11.678 39.447 -26.008 1.000 15.73      C
ANISOU 109 C  GLY A 13   2555  1955  1468   87  357  -109    C
ATOM  110 O  GLY A 13   11.444 40.201 -26.971 1.000 20.93      O
ANISOU 110 O  GLY A 13   3837  2505  1611  164  -121  189    O
ATOM  111 N  ASN A 14   11.608 39.863 -24.755 1.000 13.68      N
ANISOU 111 N  ASN A 14   2059  1674  1462   27  244  -96    N

Relationships to Other Record Types

The standard deviations for the anisotropic temperature factors are related to the corresponding ATOM/ HETATM ANISOU temperature factors.

Example

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM  107 N  GLY A 13   12.681 37.302 -25.211 1.000 15.56      N
ANISOU 107 N  GLY A 13   2406  1892  1614  198  519  -328    N
SIGUIJ 107 N  GLY A 13    10   10   10   10  10   10    N
ATOM  108 CA GLY A 13   11.982 37.996 -26.241 1.000 16.92     C
ANISOU 108 CA GLY A 13  2748  2004  1679  -21  155  -419    C
SIGUIJ 108 CA GLY A 13    10   10   10   10  10   10    C
ATOM  109 C  GLY A 13   11.678 39.447 -26.008 1.000 15.73     C
ANISOU 109 C  GLY A 13   2555  1955  1468   87  357  -109    C
SIGUIJ 109 C  GLY A 13    10   10   10   10  10   10    C
ATOM  110 O  GLY A 13   11.444 40.201 -26.971 1.000 20.93     O
ANISOU 110 O  GLY A 13   3837  2505  1611  164  -121  189    O
SIGUIJ 110 O  GLY A 13    10   10   10   10  10   10    O
ATOM  111 N  ASN A 14   11.608 39.863 -24.755 1.000 13.68     N
ANISOU 111 N  ASN A 14   2059  1674  1462   27  244  -96    N
SIGUIJ 111 N  ASN A 14    10   10   10   10  10   10    N

TER

Overview

The TER record indicates the end of a list of ATOM/HETATM records for a chain.

Record Format

COLUMNS    DATA TYPE  FIELD      DEFINITION
-------------------------------------------------------------------------
 1 - 6    Record name  "TER  "
 7 - 11    Integer    serial     Serial number.
18 - 20    Residue name resName     Residue name.
22       Character   chainID     Chain identifier.
23 - 26    Integer    resSeq     Residue sequence number.
27       AChar     iCode      Insertion code.

Details

Every chain of ATOM/HETATM records presented on SEQRES records is terminated with a TER record.
The TER records occur in the coordinate section of the entry, and indicate the last residue presented for each polypeptide and/or nucleic acid chain for which there are determined coordinates. For proteins, the residue defined on the TER record is the carboxy-terminal residue; for nucleic acids it is the 3'-terminal residue.
For a cyclic molecule, the choice of termini is arbitrary.
Terminal oxygen atoms are presented as OXT for proteins, and as O5’ or OP3 for nucleic acids. These atoms are present only if the last residue in the polymer is truly the last residue in the SEQRES.
The TER record has the same residue name, chain identifier, sequence number and insertion code as the terminal residue. The serial number of the TER record is one number greater than the serial number of the ATOM/HETATM preceding the TER.

Verification/Validation/Value Authority Control

TER must appear at the terminal carboxyl end or 3' end of a chain. For proteins, there is usually a terminal oxygen, labeled OXT. The validation program checks for the occurrence of TER and OXT records.

Relationships to Other Record Types

The residue name appearing on the TER record must be the same as the residue name of the immediately preceding ATOM or non-water HETATM record.

Example

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM  601 N  LEU A 75   -17.070 -16.002  2.409 1.00 55.63      N 
ATOM  602 CA LEU A 75   -16.343 -16.746  3.444 1.00 55.50      C 
ATOM  603 C  LEU A 75   -16.499 -18.263  3.300 1.00 55.55      C 
ATOM  604 O  LEU A 75   -16.645 -18.789  2.195 1.00 55.50      O 
ATOM  605 CB LEU A 75   -16.776 -16.283  4.844 1.00 55.51      C 
TER   606   LEU A 75  
... ... 
ATOM  1185 O  LEU B 75   26.292 -4.310 16.940 1.00 55.45      O 
ATOM  1186 CB LEU B 75   23.881 -1.551 16.797 1.00 55.32      C 
TER  1187   LEU B 75                           
HETATM 1188 H2 SRT A1076   -17.263 11.260 28.634 1.00 59.62      H 
HETATM 1189 HA SRT A1076   -19.347 11.519 28.341 1.00 59.42      H 
HETATM 1190 H3 SRT A1076   -17.157 14.303 28.677 1.00 58.00      H 
HETATM 1191 HB SRT A1076   -15.110 13.610 28.816 1.00 57.77      H 
HETATM 1192 O1 SRT A1076   -17.028 11.281 31.131 1.00 62.63      O 
ATOM  295 HB2 ALA A 18   4.601 -9.393  7.275 1.00 0.00      H 
ATOM  296 HB3 ALA A 18    3.340 -9.147  6.043 1.00 0.00      H 
TER   297   ALA A 18                           
ENDMDL

HETATM

Overview

Non-polymer or other "non-standard" chemical coordinates, such as water molecules or atoms presented in HET groups use the HETATM record type. They also present the occupancy and temperature factor for each atom. The ATOM records present the atomic coordinates for standard residues. The element symbol is always present on each HETATM record; charge is optional.

Changes in ATOM/HETATM records will require standardization in atom and residue nomenclature. This nomenclature is described in the Chemical Component Dictionary, https://files.wwpdb.org/pub/pdb/data/monomers.

Record Format

COLUMNS    DATA TYPE   FIELD     DEFINITION
-----------------------------------------------------------------------
 1 - 6    Record name  "HETATM"
 7 - 11    Integer    serial    Atom serial number.
13 - 16    Atom      name     Atom name.
17      Character   altLoc    Alternate location indicator.
18 - 20    Residue name  resName    Residue name.
22      Character   chainID    Chain identifier.
23 - 26    Integer    resSeq    Residue sequence number.
27      AChar     iCode     Code for insertion of residues.
31 - 38    Real(8.3)   x       Orthogonal coordinates for X.
39 - 46    Real(8.3)   y       Orthogonal coordinates for Y.
47 - 54    Real(8.3)   z       Orthogonal coordinates for Z.
55 - 60    Real(6.2)   occupancy   Occupancy.
61 - 66    Real(6.2)   tempFactor  Temperature factor.
77 - 78    LString(2)   element    Element symbol; right-justified.
79 - 80    LString(2)   charge    Charge on the atom.

Details

The x, y, z coordinates are in Angstrom units.
No ordering is specified for polysaccharides.
See the HET section of this document regarding naming of heterogens. See the Chemical Component Dictionary for residue names, formulas, and topology of the HET groups that have appeared so far in the PDB (see https://files.wwpdb.org/pub/pdb/data/monomers ).
If the depositor provides the data, then the isotropic B value is given for the temperature factor.
If there are neither isotropic B values provided by the depositor, nor anisotropic temperature factors in ANISOU, then the default value of 0.0 is used for the temperature factor.
Insertion codes and element naming are fully described in the ATOM section of this document.

Verification/Validation/Value Authority Control

Processing programs check ATOM/HETATM records for PDB file format, sequence information, and packing.

Relationships to Other Record Types

HETATM records must have corresponding HET, HETNAM, FORMUL and CONECT records, except for waters.

Example

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HETATM 8237 MG  MG A1001   13.872 -2.555 -29.045 1.00 27.36     MG 
 
HETATM 3835 FE  HEM A  1   17.140  3.115 15.066 1.00 14.14     FE
HETATM 8238 S  SO4 A2001   10.885 -15.746 -14.404 1.00 47.84      S 
HETATM 8239 O1 SO4 A2001   11.191 -14.833 -15.531 1.00 50.12      O 
HETATM 8240 O2 SO4 A2001    9.576 -16.338 -14.706 1.00 48.55      O 
HETATM 8241 O3 SO4 A2001   11.995 -16.703 -14.431 1.00 49.88     O 
HETATM 8242 O4 SO4 A2001   10.932 -15.073 -13.100 1.00 49.91      O

ENDMDL

Overview

The ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry.

Record Format

COLUMNS    DATA TYPE   FIELD    DEFINITION
------------------------------------------------------------------
1 - 6     Record name  "ENDMDL"

Details

MODEL/ENDMDL records are used only when more than one structure is presented in the entry, as is often the case with NMR entries.
All the models in a multi-model entry must represent the same structure.
Every MODEL record has an associated ENDMDL record.

Verification/Validation/Value Authority Control

Entries with multiple structures in the NUMMDL record are checked for corresponding pairs of MODEL/ ENDMDL records, and for consecutively numbered models.

Relationships to Other Record Types

There must be a corresponding MODEL record.

In the case of an NMR entry, the NUMMDL record states the number of model structures that are present in the individual entry.

Example

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
... ...
... ...
ATOM 14550 1HG GLU  122   -14.364 14.787 -14.258 1.00 0.00      H
ATOM 14551 2HG GLU  122   -13.794 13.738 -12.961 1.00 0.00      H
TER  14552   GLU  122                       
ENDMDL                                 
MODEL    9                             
ATOM 14553 N  SER   1   -28.280  1.567 12.004 1.00 0.00      N
ATOM 14554 CA SER   1   -27.749  0.392 11.256 1.00 0.00      C
... ...
... ...
ATOM 16369 1HG GLU  122   -3.757 18.546 -8.439 1.00 0.00      H
ATOM 16370 2HG GLU  122   -3.066 17.166 -7.584 1.00 0.00      H
TER  16371   GLU  122                       
ENDMDL