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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3bjw
HYDROLASE HEADER
CRYSTAL STRUCTURE OF ECARPHOLIN S COMPLEXED WITH SURAMIN 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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SVR B 512
1A SER
2A VAL
3A VAL
7B LYS
10B ILE
11B GLN
12B GLU
13B THR
14B GLY
16G LYS
19A PHE
21G SER
23A THR
69A LYS
70A THR
72B ARG
107B ARG
110B LEU
111B ASN
112G THR
113G TYR
114G ASN
115G LYS
116G LYS
117G TYR
119G TYR
120G TYR
121G PRO
124G PHE
125G TRP
SVR C 507
1F SER
2F VAL
3C VAL
4C GLU
5C LEU
6C GLY
7C LYS
9C ILE
10C ILE
11F GLN
17F SER
18C PRO
19F PHE
23C THR
30C GLY
35D GLY
36D PRO
38D LEU
69C LYS
70F THR
72C ARG
74C LYS
77F ARG
79F ASN
80F GLY
121B PRO
124B PHE
125B TRP
126D CYS
127B LYS
128D GLY
SVR F 509
1C SER
2C VAL
3C VAL
7F LYS
10F ILE
11F GLN
12F GLU
13F THR
14F GLY
16D LYS
19C PHE
21D SER
23C THR
69C LYS
70C THR
72F ARG
107F ARG
110F LEU
111F ASN
113D TYR
114D ASN
115D LYS
116D LYS
117D TYR
119D TYR
120D TYR
121D PRO
124D PHE
125D TRP
SVR A 508
1E SER
2E VAL
3G VAL
4G GLU
5G LEU
6G GLY
7G LYS
9G ILE
10G ILE
11E GLN
17E SER
18G PRO
19E PHE
22G TYR
23G THR
30G GLY
36A PRO
69G LYS
70E THR
72G ARG
74G LYS
77E ARG
80E GLY
121H PRO
124H PHE
125H TRP
127H LYS
128A GLY
SVR E 510
1G SER
2G VAL
3E VAL
7E LYS
10E ILE
11E GLN
12E GLU
13E THR
14E GLY
16A LYS
19G PHE
21A SER
23G THR
69G LYS
70G THR
72E ARG
107E ARG
110E LEU
111E ASN
113A TYR
114A ASN
115A LYS
116A LYS
117A TYR
119A TYR
120A TYR
121A PRO
124A PHE
125A TRP
SVR C 505
1H SER
2H VAL
3D VAL
4D GLU
5D LEU
6D GLY
7D LYS
10D ILE
11H GLN
17H SER
18D PRO
19H PHE
23D THR
27C CYS
30D GLY
35C GLY
36C PRO
38C LEU
69D LYS
70H THR
72D ARG
74D LYS
77H ARG
78H GLU
80H GLY
121E PRO
124E PHE
125E TRP
127E LYS
128C GLY
SVR H 511
1D SER
2D VAL
3H VAL
7H LYS
10H ILE
11H GLN
12H GLU
13H THR
14H GLY
16C LYS
19D PHE
21C SER
23D THR
69D LYS
70D THR
72H ARG
107H ARG
110H LEU
111H ASN
113C TYR
114C ASN
115C LYS
116C LYS
117C TYR
121C PRO
124C PHE
125C TRP
SVR B 501
2B VAL
3B VAL
5B LEU
6B GLY
7B LYS
9B ILE
10B ILE
16B LYS
17B SER
18B PRO
19B PHE
20B PRO
21B SER
23B THR
30B GLY
115F LYS
116F LYS
119F TYR
120F TYR
121F PRO
122F ASN
124F PHE
125F TRP
SVR G 506
2B VAL
3A VAL
4A GLU
5A LEU
6A GLY
7A LYS
10A ILE
11B GLN
17B SER
18A PRO
19B PHE
23A THR
30A GLY
36G PRO
38G LEU
69B LYS
70B THR
72A ARG
74A LYS
77B ARG
121F PRO
124F PHE
125F TRP
127F LYS
128G GLY
SVR F 502
2F VAL
3C VAL
5F LEU
6F GLY
7F LYS
9F ILE
10F ILE
16F LYS
17F SER
18F PRO
19F PHE
20F PRO
21C SER
23F THR
30F GLY
115C LYS
116B LYS
119B TYR
120B TYR
121B PRO
122B ASN
124B PHE
125B TRP
SVR E 503
2E VAL
3G VAL
5E LEU
6E GLY
7E LYS
9E ILE
10E ILE
16E LYS
17E SER
18E PRO
19E PHE
20E PRO
21E SER
23E THR
30E GLY
115H LYS
116H LYS
119H TYR
120H TYR
121H PRO
122H ASN
124H PHE
125H TRP
SVR H 504
2H VAL
3H VAL
5H LEU
6H GLY
7H LYS
9H ILE
10H ILE
16H LYS
17H SER
18H PRO
19H PHE
20H PRO
21H SER
23H THR
30H GLY
115E LYS
116E LYS
119E TYR
120E TYR
121E PRO
122E ASN
124E PHE
125E TRP
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):

» Jmol
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
2qhe Details
other holo-structures
pdb ID Ligand Unique ID
2qhd DAOA_501 Details
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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SVR NAME: 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC
FORMULA: C51 H40 N6 O23 S6
SMILES: Cc1ccc(cc1NC(=O)c2cccc(NC(=O)Nc3cccc(c3)C(=O)Nc4cc(ccc4C)C(=O)Nc5ccc(c6cc(cc(c56)S(O)(=O)=O)S(O)(=O)=O)S(O)(=O)=O)c2)C(=O)Nc7ccc(c8cc(cc(c78)S(O)(=O)=O)S(O)(=O)=O)S(O)(=O)=O
v4.0
May 2008
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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