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

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
none
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
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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