Data Items Describing Atomic Positions

Cartesian coordinate data in PDB entries are stored in the ATOM_SITE category. Atomic positions are uniquely identified by the data item _atom_site.id. A typical atomic position for a macromolecule includes a variety of label information. The data items which label atomic positions can be divided into two groups: those that are integrated into higher level structural descriptions and those that are provided to hold a particular choice of nomenclature such as the nomenclature used by the PDB. These distinctions are noted in the following list of the data items used to describe atomic positions. This is followed by a diagram illustrating data categories related to the ATOM_SITE category and an example from a recent PDB data file.

_atom_site.id: A unique identifier for each atom position.
_atom_site.type_symbol: The atom type.
_atom_site.auth_asym_id: This data item is an author defined alternative to the value of _atom_site.label_asym_id. This item holds the PDB chain identifier.
_atom_site.auth_atom_id: This data item is an author defined alternative to the value of _atom_site.label_atom_id. This item holds the PDB atom name.
_atom_site.auth_comp_id: This data item is an author defined alternative to the value of _atom_site.label_comp_id. This item holds the PDB 3-letter-code residue names
_atom_site.auth_seq_id: This data item is an author defined alternative to the value of _atom_site.label_seq_id. This item holds the PDB residue number.
_atom_site.pdbx_PDB_ins_code: This data item corresponds to the PDB insertion code.
_atom_site.pdbx_PDB_model_num: This data item identifies the model number in an ensemble of coordinate data.
_atom_site.group_PDB: This data item is a place holder for the tags used by the PDB to identify coordinate records (e.g. ATOM or HETATM).
_atom_site.label_alt_id: This item is a uniquely identifies for each alternative site for this atom position.
_atom_site.label_asym_id: This data item is reference to item _struct_asym.id defined in category STRUCT_ASYM. This item identifies an instance of particular entity in the deposited coordinate set. For a structure determined by crystallographic method this corresponds to a unique identifier within the cyrstallographic asymmetric unit.
_atom_site.label_atom_id: This data item is a reference to item _chem_comp_atom.atom_id defined in category CHEM_COMP_ATOM which is stored in the Chemical Component Dictionary. This atom identifier uniquely identifies each atom within each chemical component.
_atom_site.label_comp_id: This data item is a reference to item _chem_comp.id defined in category CHEM_COMP. This item is the primary identifier for chemical components which may either be mononers in a polymeric entity or complete non-polymer entities.
_atom_site.label_entity_id: This data item is a reference to _entity.id defined in the ENTITY category. This item is used to identify chemically distinct portions of the molecular structure (e.g. polymer chains, ligands, solvent).
_atom_site.label_seq_id: This data item is a reference to _entity_poly_seq.num defined in the ENTITY_POLY_SEQ category. This item is used to maintain the correspondence between the chemical sequence of a polymeric entity and the sequence information in the coordinate list and in may other structural categories. This identifier has no meaning for non-polymer entities.
_atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z: Cartesian coordinate components describing the position of this atom site.
_atom_site.B_iso_or_equiv: Isotropic atomic displacement parameter
_atom_site.occupancy: The fraction of the atom present at this atom position.
_atom_site.pdbx_formal_charge: The net integer charge assigned to this atom.
_atom_site.*_esd: Optional uncertainties assoicated with coordinate positions, occupancies and temperature factors.

Data Category Relationships for the ATOM_SITE Category

Click-on data items in the figure to navigate to more details about the item.

ATOM_SITE Data Entry Example

The following is an abbreviated example of a typical ATOM_SITE category found in current PDB entries.

#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_alt_id
_atom_site.label_comp_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.label_seq_id
_atom_site.pdbx_PDB_ins_code
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x_esd
_atom_site.Cartn_y_esd
_atom_site.Cartn_z_esd
_atom_site.occupancy_esd
_atom_site.B_iso_or_equiv_esd
_atom_site.pdbx_formal_charge
_atom_site.auth_seq_id
_atom_site.auth_comp_id
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.pdbx_PDB_model_num
ATOM   1    N  N     . PRO A 1 5   ? -3.218  23.313  19.768  1.00 65.32  ? ? ? ? ? ? 4   PRO A N     1
ATOM   2    C  CA    . PRO A 1 5   ? -2.926  24.681  19.350  1.00 62.03  ? ? ? ? ? ? 4   PRO A CA    1
ATOM   3    C  C     . PRO A 1 5   ? -3.532  24.954  17.967  1.00 52.41  ? ? ? ? ? ? 4   PRO A C     1
ATOM   4    O  O     . PRO A 1 5   ? -4.356  24.167  17.505  1.00 67.03  ? ? ? ? ? ? 4   PRO A O     1
ATOM   5    C  CB    . PRO A 1 5   ? -1.419  24.648  19.202  1.00 43.04  ? ? ? ? ? ? 4   PRO A CB    1
ATOM   6    C  CG    . PRO A 1 5   ? -1.192  23.263  18.562  1.00 39.23  ? ? ? ? ? ? 4   PRO A CG    1
ATOM   7    C  CD    . PRO A 1 5   ? -2.288  22.354  19.126  1.00 51.55  ? ? ? ? ? ? 4   PRO A CD    1
ATOM   8    N  N     . ALA A 1 6   ? -3.090  26.021  17.294  1.00 52.98  ? ? ? ? ? ? 5   ALA A N     1
ATOM   9    C  CA    . ALA A 1 6   ? -3.728  26.465  16.035  1.00 51.88  ? ? ? ? ? ? 5   ALA A CA    1
ATOM   10   C  C     . ALA A 1 6   ? -3.377  25.670  14.766  1.00 46.85  ? ? ? ? ? ? 5   ALA A C     1
ATOM   11   O  O     . ALA A 1 6   ? -2.231  25.220  14.574  1.00 49.84  ? ? ? ? ? ? 5   ALA A O     1
ATOM   12   C  CB    . ALA A 1 6   ? -3.468  27.944  15.798  1.00 63.69  ? ? ? ? ? ? 5   ALA A CB    1
ATOM   13   N  N     . PHE A 1 7   ? -4.377  25.540  13.893  1.00 37.09  ? ? ? ? ? ? 6   PHE A N     1
ATOM   14   C  CA    . PHE A 1 7   ? -4.229  24.943  12.577  1.00 45.06  ? ? ? ? ? ? 6   PHE A CA    1
ATOM   15   C  C     . PHE A 1 7   ? -4.984  25.738  11.542  1.00 51.31  ? ? ? ? ? ? 6   PHE A C     1
ATOM   16   O  O     . PHE A 1 7   ? -6.218  25.714  11.526  1.00 55.98  ? ? ? ? ? ? 6   PHE A O     1
ATOM   17   C  CB    . PHE A 1 7   ? -4.741  23.508  12.537  1.00 36.00  ? ? ? ? ? ? 6   PHE A CB    1
ATOM   18   C  CG    . PHE A 1 7   ? -4.685  22.898  11.159  1.00 41.66  ? ? ? ? ? ? 6   PHE A CG    1
ATOM   19   C  CD1   . PHE A 1 7   ? -3.468  22.549  10.588  1.00 33.97  ? ? ? ? ? ? 6   PHE A CD1   1
ATOM   20   C  CD2   . PHE A 1 7   ? -5.841  22.688  10.408  1.00 50.94  ? ? ? ? ? ? 6   PHE A CD2   1
ATOM   21   C  CE1   . PHE A 1 7   ? -3.397  21.958  9.319   1.00 43.65  ? ? ? ? ? ? 6   PHE A CE1   1
ATOM   22   C  CE2   . PHE A 1 7   ? -5.778  22.106  9.140   1.00 45.19  ? ? ? ? ? ? 6   PHE A CE2   1
ATOM   23   C  CZ    . PHE A 1 7   ? -4.563  21.730  8.592   1.00 49.00  ? ? ? ? ? ? 6   PHE A CZ    1
# ----   Abbreviated ---
HETATM 4164 P  PG    . ATP C 2 .   ? 20.962  12.011  1.365   1.00 41.32  ? ? ? ? ? ? 401 ATP A PG    1
HETATM 4165 O  O1G   . ATP C 2 .   ? 21.393  12.110  -0.112  1.00 43.12  ? ? ? ? ? ? 401 ATP A O1G   1
HETATM 4166 O  O2G   . ATP C 2 .   ? 21.639  12.985  2.323   1.00 44.84  ? ? ? ? ? ? 401 ATP A O2G   1
HETATM 4167 O  O3G   . ATP C 2 .   ? 20.909  10.573  1.847   1.00 37.48  ? ? ? ? ? ? 401 ATP A O3G   1
HETATM 4168 P  PB    . ATP C 2 .   ? 18.271  11.978  0.572   1.00 34.91  ? ? ? ? ? ? 401 ATP A PB    1
HETATM 4169 O  O1B   . ATP C 2 .   ? 18.090  12.728  -0.675  1.00 29.20  ? ? ? ? ? ? 401 ATP A O1B   1
HETATM 4170 O  O2B   . ATP C 2 .   ? 18.341  10.456  0.534   1.00 34.09  ? ? ? ? ? ? 401 ATP A O2B   1
HETATM 4171 O  O3B   . ATP C 2 .   ? 19.495  12.655  1.349   1.00 45.36  ? ? ? ? ? ? 401 ATP A O3B   1
HETATM 4172 P  PA    . ATP C 2 .   ? 16.452  11.937  3.022   1.00 33.03  ? ? ? ? ? ? 401 ATP A PA    1
HETATM 4173 O  O1A   . ATP C 2 .   ? 17.575  11.008  3.414   1.00 46.96  ? ? ? ? ? ? 401 ATP A O1A   1
HETATM 4174 O  O2A   . ATP C 2 .   ? 15.848  13.185  3.662   1.00 29.30  ? ? ? ? ? ? 401 ATP A O2A   1
HETATM 4175 O  O3A   . ATP C 2 .   ? 16.996  12.454  1.545   1.00 38.09  ? ? ? ? ? ? 401 ATP A O3A   1
HETATM 4176 O  "O5'" . ATP C 2 .   ? 15.189  11.074  2.488   1.00 30.64  ? ? ? ? ? ? 401 ATP A "O5'" 1
HETATM 4177 C  "C5'" . ATP C 2 .   ? 13.823  11.342  2.799   1.00 37.28  ? ? ? ? ? ? 401 ATP A "C5'" 1
HETATM 4178 C  "C4'" . ATP C 2 .   ? 12.972  10.344  2.002   1.00 26.45  ? ? ? ? ? ? 401 ATP A "C4'" 1
HETATM 4179 O  "O4'" . ATP C 2 .   ? 13.120  10.724  0.616   1.00 28.76  ? ? ? ? ? ? 401 ATP A "O4'" 1
HETATM 4180 C  "C3'" . ATP C 2 .   ? 13.415  8.897   2.065   1.00 24.11  ? ? ? ? ? ? 401 ATP A "C3'" 1
HETATM 4181 O  "O3'" . ATP C 2 .   ? 12.190  8.163   2.027   1.00 22.56  ? ? ? ? ? ? 401 ATP A "O3'" 1
HETATM 4182 C  "C2'" . ATP C 2 .   ? 14.141  8.665   0.734   1.00 31.42  ? ? ? ? ? ? 401 ATP A "C2'" 1
HETATM 4183 O  "O2'" . ATP C 2 .   ? 14.068  7.317   0.162   1.00 24.72  ? ? ? ? ? ? 401 ATP A "O2'" 1
HETATM 4184 C  "C1'" . ATP C 2 .   ? 13.378  9.576   -0.172  1.00 24.75  ? ? ? ? ? ? 401 ATP A "C1'" 1
HETATM 4185 N  N9    . ATP C 2 .   ? 14.113  9.918   -1.390  1.00 30.65  ? ? ? ? ? ? 401 ATP A N9    1
HETATM 4186 C  C8    . ATP C 2 .   ? 15.373  10.446  -1.439  1.00 35.62  ? ? ? ? ? ? 401 ATP A C8    1
HETATM 4187 N  N7    . ATP C 2 .   ? 15.777  10.600  -2.734  1.00 32.13  ? ? ? ? ? ? 401 ATP A N7    1
HETATM 4188 C  C5    . ATP C 2 .   ? 14.741  10.181  -3.516  1.00 28.00  ? ? ? ? ? ? 401 ATP A C5    1
HETATM 4189 C  C6    . ATP C 2 .   ? 14.493  10.020  -4.949  1.00 28.13  ? ? ? ? ? ? 401 ATP A C6    1
HETATM 4190 N  N6    . ATP C 2 .   ? 15.464  10.410  -5.770  1.00 30.25  ? ? ? ? ? ? 401 ATP A N6    1
HETATM 4191 N  N1    . ATP C 2 .   ? 13.289  9.525   -5.366  1.00 24.00  ? ? ? ? ? ? 401 ATP A N1    1
HETATM 4192 C  C2    . ATP C 2 .   ? 12.339  9.118   -4.478  1.00 25.99  ? ? ? ? ? ? 401 ATP A C2    1
HETATM 4193 N  N3    . ATP C 2 .   ? 12.536  9.204   -3.144  1.00 21.86  ? ? ? ? ? ? 401 ATP A N3    1
HETATM 4194 C  C4    . ATP C 2 .   ? 13.665  9.718   -2.625  1.00 34.62  ? ? ? ? ? ? 401 ATP A C4    1
# ----   Abbreviated ---