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Categories that define the chemical structure and nomenclature of the momoners and ligands in the experiment.
Category chem_comp
_chem_comp.pdbx_pcm
A flag to indicate if the CCD can be used to represent a protein modification.
Attribute
Key
Required
Type
Units
Enumerated
Bounded
pdbx_pcm
no
no
code
None
yes
no
Allowed Values
Detail
Y
Yes - Can be used to represent a protein modification
N
No - Should never be used to represent a protein modification
Category chem_comp_atom
_chem_comp.pdbx_backbone_atom_flag
A flag indicating the backbone atoms in polypeptide units.
Attribute
Key
Required
Type
Units
Enumerated
Bounded
pdbx_backbone_atom_flag
no
no
code
None
yes
no
Allowed Values
Detail
Y
Yes - a part of the polypeptide backbone
N
No - not part of the polypeptide backbone
_chem_comp.pdbx_n_terminal_atom_flag
A flag indicating the N-terminal group atoms in polypeptide units.
Attribute
Key
Required
Type
Units
Enumerated
Bounded
pdbx_n_terminal_atom_flag
no
no
code
None
yes
no
Allowed Values
Detail
Y
Yes - a part of the N-terminal group
N
No - not part of the N-terminal group
_chem_comp.pdbx_c_terminal_atom_flag
A flag indicating the C-terminal group atoms in polypeptide units.
Attribute
Key
Required
Type
Units
Enumerated
Bounded
pdbx_c_terminal_atom_flag
no
no
code
None
yes
no
Allowed Values
Detail
Y
Yes - a part of the C-terminal group
N
No - not part of the C-terminal group
Category pdbx_chem_comp_pcm
Data items in the PDBX_CHEM_COMP_PCM category provide information about the
protein modifications that are described by the chemical component.
Example 1:
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 SEP SER Phosphorylation "Named protein modification" "Amino-acid side chain" "Any position" . . PTM-0253 ?
Example 2:
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 FUC SER None Carbohydrate "Amino-acid side chain" "Any position" C1 OG ? ?
2 FUC THR None Carbohydrate "Amino-acid side chain" "Any position" C1 OG1 ? ?
Attribute
Key
Required
Type
Units
Enumerated
Bounded
pcm_id
yes
yes
int
None
no
no
comp_id
no
yes
ucode
None
no
no
modified_residue_id
no
no
uline
None
no
no
type
no
yes
line
None
yes
no
category
no
yes
line
None
yes
no
position
no
yes
line
None
yes
no
polypeptide_position
no
yes
line
None
yes
no
comp_id_linking_atom
no
no
atcode
None
no
no
modified_residue_id_linking_atom
no
no
atcode
None
no
no
uniprot_specific_ptm_accession
no
no
uniprot_ptm_id
None
no
no
uniprot_generic_ptm_accession
no
no
uniprot_ptm_id
None
no
no
_pdbx_chem_comp_pcm.pcm_id
An ordinal index for this category.
_pdbx_chem_comp_pcm.comp_id
Chemical component identifier for the CCD that contains the modification group.
_pdbx_chem_comp_pcm.modified_residue_id
Chemical component identifier for the amino acid residue that is being modified.
_pdbx_chem_comp_pcm.type
The type of protein modification.
Allowed Values
Details
ADP-ribosylation
.
AMPylation
.
Acetamidation
.
Acetylation
.
Allysine
.
...
.
Sulfonation
.
Tert-butylation
.
Thyroxine
.
Triiodothyronine
.
UMPylation
.
_pdbx_chem_comp_pcm.category
The category of protein modification.
Allowed Values
Details
ADP-Ribose
ADP-ribose protein modifications
Amino acid
Canonical amino acid linked to a peptide residue
Biotin
Biotin protein modifications
Carbohydrate
Carbohydrate protein modifications
Chromophore/chromophore-like
Chromophore or chromophore-like protein modifications
Covalent chemical modification
A diverse range of chemical compounds that form covalent bonds with amino acids. Not covered by any of the other modification categories
Crosslinker
Chemical modifications which covalently link two amino-acid residues. Excludes reaction intermediates and modifications covered by other modification categories
Flavin
Flavin protein modifications
Heme/heme-like
Heme or heme-like protein modifications
Lipid/lipid-like
Lipid or lipid-like protein modifications
Named protein modification
All protein modifications that are well defined into known types, have limited diversity, and are not explicitly covered by any other category. It includes PTMs, PCMs, rare amino acids and unnatural amino acids
Non-standard residue
A diverse range of non-standard polypeptide residues that are not considered to be 'Named protein modifications'. These cannot be practically split into two CCDs, which describe the standard polypeptide residue and the modification group, and are not covered by any of the other modification categories
Nucleotide monophosphate
Nucleotide monophosphate protein modifications
Terminal acetylation
Terminal acetylation protein modification
Terminal amidation
Terminal amidation protein modification
_pdbx_chem_comp_pcm.position
The position of the modification on the amino acid.
Allowed Values
Detail
Amino-acid side chain
Protein modification occurs on the amino acid side chain
Amino-acid backbone
Protein modification occurs on the amino acid backbone
Amino-acid side chain and backbone
Protein modification occurs on both the amino acid side chain and backbone
_pdbx_chem_comp_pcm.polypeptide_position
The position of the modification on the polypeptide.
Allowed Values
Detail
C-terminal
Protein modification can only occur on C-terminus
N-terminal
Protein modification can only occur on N-terminus
Any position
Protein modification can occur in any position of the polypeptide sequence
_pdbx_chem_comp_pcm.comp_id_linking_atom
The atom on the modification group that covalently links the
modification to the residue that is being modified. This is
only added when the protein modification is linked and so the
amino acid group and the modification group are described by
separate CCDs.
The atom on the polypeptide residue group that covalently links
the modification to the residue that is being modified. This is
only added when the protein modification is linked and so the
amino acid group and the modification group are described by
separate CCDs.
The UniProt PTM accession code that is an exact match for the protein modification.
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
The UniProt PTM accession code that describes the group of PTMs of which this protein modification is a member.
Category Group entry_group
Category pdbx_entry_details
_pdbx_entry_details.has_protein_modification
A flag to indicate if the model contains any protein modifications.
Attribute
Key
Required
Type
Units
Enumerated
Bounded
has_protein_modification
no
no
code
None
yes
no
Allowed Values
Detail
Y
Protein modification present
Category pdbx_modification_feature
Data items in the PDBX_MODIFICATION_FEATURE category provides
information about all the protein modifications that have been
modeled in the entry.
Example 1 - An example of the category in an entry that contains a disulfide bridge and
two phosphoserine modifications.
loop_
_pdbx_modification_feature.ordinal
_pdbx_modification_feature.label_comp_id
_pdbx_modification_feature.label_asym_id
_pdbx_modification_feature.label_seq_id
_pdbx_modification_feature.label_alt_id
_pdbx_modification_feature.modified_residue_label_comp_id
_pdbx_modification_feature.modified_residue_label_asym_id
_pdbx_modification_feature.modified_residue_label_seq_id
_pdbx_modification_feature.modified_residue_label_alt_id
_pdbx_modification_feature.auth_comp_id
_pdbx_modification_feature.auth_asym_id
_pdbx_modification_feature.auth_seq_id
_pdbx_modification_feature.PDB_ins_code
_pdbx_modification_feature.symmetry
_pdbx_modification_feature.modified_residue_auth_comp_id
_pdbx_modification_feature.modified_residue_auth_asym_id
_pdbx_modification_feature.modified_residue_auth_seq_id
_pdbx_modification_feature.modified_residue_PDB_ins_code
_pdbx_modification_feature.modified_residue_symmetry
_pdbx_modification_feature.comp_id_linking_atom
_pdbx_modification_feature.modified_residue_id_linking_atom
_pdbx_modification_feature.modified_residue_id
_pdbx_modification_feature.ref_pcm_id
_pdbx_modification_feature.ref_comp_id
_pdbx_modification_feature.type
_pdbx_modification_feature.category
1 SEP A 65 ? . . . . SEP A 65 ? 1_555 . . . . . . . SER 1 SEP Phosphorylation 'Named protein modification'
2 SEP B 65 ? . . . . SEP B 65 ? 1_555 . . . . . . . SER 1 SEP Phosphorylation 'Named protein modification'
3 CYS A 46 ? CYS B 46 ? CYS A 46 ? 1_555 CYS B 46 ? 1_555 SG SG . . . None 'Disulfide bridge'
Example 2 - An example of the category in an entry that contains a two cysteine
hydroxylation modification sites and two palmitoylation modification sites.
loop_
_pdbx_modification_feature.ordinal
_pdbx_modification_feature.label_comp_id
_pdbx_modification_feature.label_asym_id
_pdbx_modification_feature.label_seq_id
_pdbx_modification_feature.label_alt_id
_pdbx_modification_feature.modified_residue_label_comp_id
_pdbx_modification_feature.modified_residue_label_asym_id
_pdbx_modification_feature.modified_residue_label_seq_id
_pdbx_modification_feature.modified_residue_label_alt_id
_pdbx_modification_feature.auth_comp_id
_pdbx_modification_feature.auth_asym_id
_pdbx_modification_feature.auth_seq_id
_pdbx_modification_feature.PDB_ins_code
_pdbx_modification_feature.symmetry
_pdbx_modification_feature.modified_residue_auth_comp_id
_pdbx_modification_feature.modified_residue_auth_asym_id
_pdbx_modification_feature.modified_residue_auth_seq_id
_pdbx_modification_feature.modified_residue_PDB_ins_code
_pdbx_modification_feature.modified_residue_symmetry
_pdbx_modification_feature.comp_id_linking_atom
_pdbx_modification_feature.modified_residue_id_linking_atom
_pdbx_modification_feature.modified_residue_id
_pdbx_modification_feature.ref_pcm_id
_pdbx_modification_feature.ref_comp_id
_pdbx_modification_feature.type
_pdbx_modification_feature.category
1 CSO C 32 ? . . . . CSO C 32 ? 1_555 . . . . . . . CYS 1 CSO Hydroxylation 'Named protein modification'
2 CSO D 32 ? . . . . CSO D 32 ? 1_555 . . . . . . . CYS 1 CSO Hydroxylation 'Named protein modification'
3 PLM E . ? CYS A 82 ? PLM A 1068 ? 1_555 CYS A 68 ? 1_555 C1 SG CYS 6 PLM Palmitoylation Lipid/lipid-like
4 PLM F . ? CYS B 82 ? PLM B 1068 ? 1_555 CYS B 68 ? 1_555 C1 SG CYS 6 PLM Palmitoylation Lipid/lipid-like
Attribute
Key
Required
Type
Units
Enumerated
Bounded
ordinal
yes
yes
int
None
no
no
label_comp_id
no
yes
ucode
None
no
no
label_asym_id
no
yes
code
None
no
no
label_seq_id
no
no
int
None
no
no
label_alt_id
no
no
code
None
no
no
modified_residue_label_comp_id
no
no
ucode
None
no
no
modified_residue_label_asym_id
no
no
code
None
no
no
modified_residue_label_seq_id
no
no
int
None
no
no
modified_residue_label_alt_id
no
no
code
None
no
no
auth_comp_id
no
no
code
None
no
no
auth_asym_id
no
no
code
None
no
no
auth_seq_id
no
no
code
None
no
no
PDB_ins_code
no
no
code
None
no
no
symmetry
no
no
symop
None
no
no
modified_residue_auth_comp_id
no
no
code
None
no
no
modified_residue_auth_asym_id
no
no
code
None
no
no
modified_residue_auth_seq_id
no
no
code
None
no
no
modified_residue_PDB_ins_code
no
no
code
None
no
no
modified_residue_symmetry
no
no
symop
None
no
no
comp_id_linking_atom
no
no
atcode
None
no
no
modified_residue_id_linking_atom
no
no
atcode
None
no
no
modified_residue_id
no
no
uline
None
no
no
ref_pcm_id
no
no
int
None
no
no
ref_comp_id
no
no
ucode
None
no
no
type
no
no
line
None
yes
no
category
no
yes
line
None
yes
no
_pdbx_modification_feature.ordinal
An ordinal index for this category.
_pdbx_modification_feature.label_comp_id
A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
_pdbx_modification_feature.label_asym_id
A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
_pdbx_modification_feature.label_seq_id
A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
_pdbx_modification_feature.label_alt_id
A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.label_comp_id in the
ATOM_SITE category.
A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.label_asym_id in the
ATOM_SITE category.
A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.label_seq_id in the
ATOM_SITE category.
A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.label_alt_id in the
ATOM_SITE category.
_pdbx_modification_feature.auth_comp_id
A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
_pdbx_modification_feature.auth_asym_id
A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
_pdbx_modification_feature.auth_seq_id
A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
_pdbx_modification_feature.PDB_ins_code
A component of the identifier for the chemical component that
describes the protein modification.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
ATOM_SITE category.
_pdbx_modification_feature.symmetry
Describes the symmetry operation that should be applied to the protein modification
group.
A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.auth_comp_id in the
ATOM_SITE category.
A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.auth_asym_id in the
ATOM_SITE category.
A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.auth_seq_id in the
ATOM_SITE category.
A component of the identifier for the chemical component that
is being modified.
This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the
ATOM_SITE category.
Describes the symmetry operation that should be applied to the chemical component that
is being modified.
_pdbx_modification_feature.comp_id_linking_atom
The atom on the modification group that covalently links the
modification to the residue that is being modified. This is
only added when the protein modification is linked and so the
amino acid group and the modification group are described by
separate CCDs.
The atom on the polypeptide residue group that covalently links
the modification to the residue that is being modified. This is
only added when the protein modification is linked and so the
amino acid group and the modification group are described by
separate CCDs.
_pdbx_modification_feature.modified_residue_id
Chemical component identifier for the amino acid residue that is being modified.
_pdbx_modification_feature.ref_pcm_id
A component of the identifier for the unique kind of protein
modification.
This data item is a pointer to _pdbx_chem_comp_pcm.pcm_id in the
CHEM_COMP_PCM category.
_pdbx_modification_feature.ref_comp_id
A component of the identifier for the unique kind of protein
modification.
This data item is a pointer to _pdbx_chem_comp_pcm.comp_id in the
CHEM_COMP_PCM category.
_pdbx_modification_feature.type
The type of protein modification.
Allowed Values
Details
ADP-ribosylation
.
AMPylation
.
Acetamidation
.
Acetylation
.
Allysine
.
...
.
Sulfonation
.
Tert-butylation
.
Thyroxine
.
Triiodothyronine
.
UMPylation
.
_pdbx_modification_feature.category
The category of protein modification.
Allowed Values
Details
ADP-Ribose
ADP-ribose protein modifications
Amino acid
Canonical amino acid linked to a peptide residue
Biotin
Biotin protein modifications
Carbohydrate
Carbohydrate protein modifications
Chromophore/chromophore-like
Chromophore or chromophore-like protein modifications
Covalent chemical modification
A diverse range of chemical compounds that form covalent bonds with amino acids. Not covered by any of the other modification categories
Crosslinker
Crosslinker protein modifications
Disulfide bridge
Disulfide bridge protein modifications
Flavin
Flavin protein modifications
Heme/heme-like
Heme or heme-like protein modifications
Isopeptide bond
Isopeptide bond protein modifications
Lipid/lipid-like
Lipid or lipid-like protein modifications
Named protein modification
All protein modifications that are well defined into known types, have limited diversity, and are not explicitly covered by any other category. It includes PTMs, PCMs, rare amino acids and unnatural amino acids
Non-standard linkage
Non-standard covalent chemical linkages directly between two polypeptide residues
Non-standard residue
A diverse range of non-standard polypeptide residues that are not considered to be 'Named protein modifications'. These cannot be practically split into two CCDs, which describe the standard polypeptide residue and the modification group, and are not covered by any of the other modification categories