Overview
The ATOM records present the atomic coordinates for standard residues. They also present the occupancy and temperature factor for each atom. Heterogen coordinates use the HETATM record type. The element symbol is always present on each ATOM record; segment identifier and charge are optional.
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.
73 - 76 LString(4) segID Segment identifier, left-justified.
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.
* No ordering is specified for polysaccharides.
* 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.
* For more information on atom naming conventions, see Appendix 3, and for residue names, see Appendix 4 and the HET section of this document
* If an atom is provided in more than one position, then a non-blank alternate location indicator must be used as the alternate location indicator for each of the positions. Within a residue all atoms that are associated with each other in a given conformation are assigned the same alternate position indicator.
* 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 whole macromolecular chain, or significant portion of a chain, having alternate sites, the atoms for each alternate position are listed together. The two conformers are delineated by MODEL/ENDMDL records. In this case each MODEL must represent the entire molecular assemblage, including any heterogen group which is not necessarily disordered. Such is the case when DNA molecules are placed in UP and DOWN positions.
- In the case of a large heterogen groups which are disordered, the atoms for each conformer are listed together. The two lists are not separated by MODEL/ENDMDL as is done for macromolecular chains.
* Addition of atoms to side chains of standard residues are handled as follows:
The additional atoms (modifying group) are represented as a HET group which is assigned its own residue name. The chainID, sequence number, and insertion code assigned to the HET group is that of the standard residue to which it is attached.
* Chemical modifications of standard residue side chains by addition of new atoms are handled as follows:
- The new atoms are represented as a HET group. This group is assigned the chain name, sequence number, and insertion code of the standard residue that it modifies.
- The atoms comprising these het groups are listed as HETATM and are inserted in the ATOM list immediately after the TER record of the chain. These groups are listed in the same order as the standard residue to which they are bonded (i.e., from the N- to C-terminus for polypeptides and from the 5' to 3' end for nucleic acids).
- Modified standard residues and the modifying het group may be assigned the same SEGID to further describe the relationship between the groups. PDB will use this mechanism only if SEGID's were not assigned to these atoms for other purposes.
- Modified standard residues must have a corresponding MODRES record.
* The insertion code is commonly used in sequence numbering and is described here. In most cases, the amino acids that comprise a protein are numbered sequentially starting with 1. However, there are a number of situations that may give rise to different numbering schemes:
- Homologous proteins can exist in a number of different species. Depositors may use a residue numbering scheme in order to preserve the homology. The reference protein may be numbered sequentially starting with 1, then the homologous protein from another species aligned to it. If residues are not present in the homologous sequence, residue numbers may be skipped so that alignment can be preserved. If additional residues are present relative to the reference protein, they may have a letter, called an insertion code, appended to the sequence number. Negative numbers and zeros are permitted if they are needed to align the N-terminus.
REFERENCE PROTEIN NUMBERING HOMOLOGOUS PROTEIN NUMBERING
---------------------------------------------------------------------
59 59
60 60
61
62 62
REFERENCE PROTEIN NUMBERING HOMOLOGOUS PROTEIN NUMBERING
---------------------------------------------------------------------
85 85
86 86
86A
86B
87 87
- The numbering of a proenzyme may be used for the enzyme following cleavage.
- The molecule studied might be a portion of the whole protein. The residue numbering scheme could show the relationship to the intact protein.
- The protein might be a mutant with residues inserted and deleted. As above, the residue numbering of the native protein could be preserved by appropriate use of gaps in the numbering and/or insertion codes.
- The nucleic acid community generally numbers structures sequentially. For double-stranded nucleic acids, entries usually use two different chain identifiers. For example, an octameric duplex would be numbered 1 - 8 for chain A, and 9 - 16 for chain B.
* If the depositor provides the data, then the isotropic B value is given for the temperature factor.
* If there is no isotropic B value from the depositor, but there is an ANISOU record with anisotropic temperature factors, then the B equivalent is stored in the tempFactor field, as calculated by:
B(eq) = 8pi**2{1/3[U(1,1) + U(2,2) + U(3,3)]}
- This will obviate the need to check if ANISOU records are present before interpreting the contents of the temperature factor field.
- In some previously released PDB entries with anisotropic temperature factors provided as ANISOU records, the temperature factor field of the corresponding ATOM or HETATM record contained the equivalent U-isotropic [U(eq)] which is calculated by:
U(eq) = 1/3[U(1,1) + U(2,2) + U(3,3)] x 10**-4
* 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.
* In some entries, the occupancy and temperature factor fields are used for other quantities. In these cases, an explanation is provided in the remarks.
* Columns 73 - 76 identify specific segments of the molecule. The segment id is a string of up to four (4) alphanumeric characters, left-justified, and may include a space, e.g., CH86, A 1, NASE. The segment itself may consist of a complete chain or a portion of a chain. The importance of this new field can be appreciated if one considers an antibody structure having two molecules in the asymmetric unit. Since each chain must have a unique chain identifier, the two heavy chains and two light chains cannot currently be labeled to indicate their nature. Segment id's of CH, VH1, VH2, VH3, CL, and VL would clearly identify regions of the chains and the relationship between them. Users of X-PLOR will be familiar with SEGID as used in the refinement application of X-PLOR.
* Columns 77 - 78 contain the atom's element symbol (as given in the periodic table), right-justified. This is especially needed because in some cases it has not been possible to follow the convention that columns 13 - 14 of the atom name contain the element symbol. The most common cases are:
- In large het groups it sometimes is not possible to follow the convention of having the first two characters be the chemical symbol and still use atom names that are meaningful to users. A example is nicotinamide adenine dinucleotide, atom names begin with an A or N, depending on which portion of the molecule they appear in, e.g., AC6 or NC6, AN1 or NN1.
- Hydrogen naming sometimes conflicts with IUPAC conventions. For example, a hydrogen named HG11 in columns 13 - 16 is differentiated from a mercury atom by the element symbol in columns 77 - 78. Columns 13 - 16 present a unique name for each atom.
* Columns 79 - 80 indicate any charge on the atom, e.g., 2+, 1-. In most cases these are blank.
Verification/Validation/Value Authority Control
PDB checks ATOM/HETATM records for PDB format, sequence information, and packing. The PDB reserves the right to return deposited coordinates to the author for transformation into PDB format.
PDB intends to verify the coordinates against the experimental structure factor data in the when available. Details on this will be forthcoming.
Relationships to Other Record Types
The ATOM records are compared to the corresponding sequence database. Residue 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. Remark 550 is used to describe the meaning assigned to any segment identifiers used.
Example
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
ATOM 145 N VAL A 25 32.433 16.336 57.540 1.00 11.92 A1 N
ATOM 146 CA VAL A 25 31.132 16.439 58.160 1.00 11.85 A1 C
ATOM 147 C VAL A 25 30.447 15.105 58.363 1.00 12.34 A1 C
ATOM 148 O VAL A 25 29.520 15.059 59.174 1.00 15.65 A1 O
ATOM 149 CB AVAL A 25 30.385 17.437 57.230 0.28 13.88 A1 C
ATOM 150 CB BVAL A 25 30.166 17.399 57.373 0.72 15.41 A1 C
ATOM 151 CG1AVAL A 25 28.870 17.401 57.336 0.28 12.64 A1 C
ATOM 152 CG1BVAL A 25 30.805 18.788 57.449 0.72 15.11 A1 C
ATOM 153 CG2AVAL A 25 30.835 18.826 57.661 0.28 13.58 A1 C
ATOM 154 CG2BVAL A 25 29.909 16.996 55.922 0.72 13.25 A1 C
Known Problems
Due to the ever-increasing size of protein structures in the PDB, the atom serial number field may soon need to be increased. An increase of one column will allow for cases where entries have more than 99,999 atoms. Only 5 digits are available for the atom serial number, but some structures have already been received with more that 99,999 atoms.
No distinction is made between ribo- and deoxyribonucleotides in the SEQRES records. These residues are identified with the same residue name (i.e., A, C, G, T, U).