university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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1ayp
HYDROLASE HEADER
A PROBE MOLECULE COMPOSED OF SEVENTEEN PERCENT OF TOTAL DIFFRACTING MATTER GIVES CORRECT SOLUTIONS IN MOLECULAR REPLACEMENT TITLE
PHOSPHOLIPASE A2 COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the number of holo-structures where the residue is in contact with a ligand.
Column 2 gives the identifier of the chain to which the residue belongs.
Column 3 gives the 3-letter amino acid code, coloured according to physico-chemical type.

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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INB B 202
2B LEU
3B VAL
5B PHE
6B HIS
9B ILE
17B ALA
18B ALA
19B LEU
21B TYR
22B GLY
23B PHE
28B CYS
29B GLY
30B VAL
31B GLY
33F ARG
44B CYS
47B HIS
48B ASP
51B TYR
52B LYS
55B GLU
62B LYS
98B PHE
115F LYS
INB D 204
2D LEU
3D VAL
5D PHE
6D HIS
9D ILE
17D ALA
18D ALA
19D LEU
21D TYR
22D GLY
23D PHE
29D GLY
30D VAL
31D GLY
33A ARG
44D CYS
47D HIS
48D ASP
51D TYR
52D LYS
55D GLU
62D LYS
98D PHE
115A LYS
INB C 203
2C LEU
3C VAL
5C PHE
6C HIS
9C ILE
17C ALA
18C ALA
21C TYR
22C GLY
23C PHE
27C HIS
29C GLY
30C VAL
31C GLY
33E ARG
44C CYS
47C HIS
48C ASP
51C TYR
52C LYS
55C GLU
62C LYS
94C ALA
98C PHE
115E LYS
INB E 205
2E LEU
3E VAL
5E PHE
6E HIS
9E ILE
17E ALA
18E ALA
19E LEU
21E TYR
22E GLY
23E PHE
27E HIS
28E CYS
29E GLY
30E VAL
31E GLY
44E CYS
47E HIS
48E ASP
49E CYS
51E TYR
52E LYS
55E GLU
56E LYS
62E LYS
98E PHE
115C LYS
INB F 206
2F LEU
3F VAL
5F PHE
6F HIS
9F ILE
17F ALA
18F ALA
19F LEU
21F TYR
22F GLY
23F PHE
27F HIS
28F CYS
29F GLY
30F VAL
31F GLY
33B ARG
44F CYS
47F HIS
48F ASP
51F TYR
52F LYS
55F GLU
62F LYS
98F PHE
115B LYS
INB A 201
2A LEU
3A VAL
5A PHE
6A HIS
9A ILE
17A ALA
18A ALA
19A LEU
21A TYR
22A GLY
23A PHE
27A HIS
28A CYS
29A GLY
30A VAL
31A GLY
44A CYS
47A HIS
48A ASP
51A TYR
52A LYS
55A GLU
62A LYS
98A PHE
115D LYS
CA B 303
27B HIS
29B GLY
31B GLY
48B ASP
CA D 307
27D HIS
29D GLY
31D GLY
48D ASP
CA C 305
27C HIS
29C GLY
31C GLY
48C ASP
CA E 309
27E HIS
29E GLY
31E GLY
48E ASP
CA F 311
27F HIS
29F GLY
31F GLY
48F ASP
CA A 301
27A HIS
29A GLY
31A GLY
48A ASP
External LinksHelp

PDB The Protein Data Bank
CSA Catalytic Site Atlas
PDBSum Overview of the macromolecular structure
CATH Protein Structure Classification
Scop Structural Classification of Proteins
Pfam Protein Families and Domains
UniProt Universal Protein Resource

LIGPLOT (only on holo-pages) is hosted at the EBI.

The LigPlot Jmol links point directly to the Jmol visualisation interface provided on the PDBSum page.

Note that due to different software used, the atomic contacts of LigPlot and LigASite do not necessarily correspond.

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Links to external databases:

LigPlot (hosted at the EBI):

Download FilesHelp

Several files are provided for download:

• The XML file defining the residue-ligand contacts; this file contains data on the apo and all holo-structures.
• The XML Schema file defining the semantics of the XML file
• 3D coordinates of the structure used in constructing LigASite (PISA structure file whenever available, PDB file otherwise.
• 3D coordinates of the combined binding residues in the apo structure
• 3D coordinates of the binding residues of the holo structure (only on the holo page)

Coordinate files are in PDB format.

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Hide table of related structures
Help

List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1bbc Details
other holo-structures
pdb ID Ligand Unique ID
1poe GELB_935 _CAB_802 Details
GELA_930 _CAA_801
1db5 6IND_200 _CAC_198 Details
6INH_200 _CAG_198
1j1a _CAG_201 BHPH2301 Details
BHPD1301 _CAG_201 BHPH2301 _CAC_201
1kqu BR4D_501 _CAC_301 Details
BR4H_501 _CAG_301
1kvo OAPC_190 _CAC_191 Details
OAPD_190 _CAD_191
OAPB_190 _CAB_191
OAPA_190 _CAA_191
OAPF_190 _CAF_191
OAPE_190 _CAE_191
1dcy I3NH1201 _CAG_198 Details
I3ND1201 _CAC_198
1db4 8IND_200 _CAC_198 Details
8INH_200 _CAG_198
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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INB NAME: 1-OCTADECYL-2-ACETAMIDO-2-DEOXY-SN-GLYCEROL-3-PHOSPHOETHYLMETHYL SULFIDE
FORMULA: C26 H54 N1 O6 P1 S1
SMILES: CCCCCCCCCCCCCCCCCCOCC(COP(O)(=O)OCCSC)NC(C)=O
CA NAME: CALCIUM ION
FORMULA: CA1
SMILES: [Ca++]
v9.7
April 2012
Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada
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