university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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Browse dataset
holo-structureHelp

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

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1w1v
HYDROLASE HEADER
CRYSTAL STRUCTURE OF S. MARCESCENS CHITINASE B IN COMPLEX WITH THE CYCLIC DIPEPTIDE INHIBITOR CYCLO-(L-ARG-L-PRO) AT 1.85 A RESOLUTION TITLE
CHITINASE B 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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ALJ T1520
10A TYR
51A PHE
96A GLY
97A TRP
142A ASP
144A GLU
184A ALA
212A MET
214A TYR
215A ASP
292A TYR
294A ARG
336A ASP
339A ILE
401A MET
403A TRP
407A GLN
ALJ K1513
10V TYR
51V PHE
96V GLY
97V TRP
142V ASP
144V GLU
184V ALA
212V MET
214V TYR
215V ASP
292V TYR
294V ARG
316V ASP
339V ILE
401V MET
403V TRP
407V GLN
GOL F1509
12A PHE
51A PHE
95A GLY
96A GLY
97A TRP
98A TYR
403A TRP
GOL J1517
97A TRP
191A PHE
215A ASP
220A TRP
481V TYR
GOL R1516
97A TRP
144A GLU
212A MET
215A ASP
220A TRP
294A ARG
316A ASP
GOL B1512
97V TRP
191V PHE
220V TRP
314V GLY
316V ASP
481A TYR
GOL H1510
97V TRP
191V PHE
215V ASP
220V TRP
294V ARG
GOL X1511
97V TRP
144V GLU
145V TYR
191V PHE
212V MET
215V ASP
GOL Y1508
145V TYR
186V ALA
187V GLY
188V GLY
190V PHE
191V PHE
212V MET
214V TYR
215V ASP
216V LEU
GOL E1500
190A PHE
220A TRP
221A GLU
239A PHE
464V GLN
479V TRP
480V GLY
481V TYR
GOL K1506
190A PHE
191A PHE
194A ARG
479V TRP
480V GLY
481V TYR
482V ILE
483V THR
484V SER
489V ASP
490V SER
491V ALA
GOL D1500
190V PHE
191V PHE
193V SER
194V ARG
479A TRP
480A GLY
481A TYR
482A ILE
483A THR
489A ASP
GOL Z1507
190V PHE
220V TRP
221V GLU
239V PHE
464A GLN
479A TRP
480A GLY
481A TYR
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

no entry
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
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
1e15 Details
other holo-structures
pdb ID Ligand Unique ID
1e6r AMIL1502 NAAK1501 NAAJ1500 Details
AMIF1501 NAAE1500 NAAD1499
1w1p GIOL1518 GOLI1510 GOLK1514 Details
GOLH1508 GOLV1512
1ur8 GDLI2502 NAGH2501 Details
GDLP2502 SO4L1510 NAGO2501
1w1y TYPJ1508 TYPQ1506 TYPN1507 Details
GOLS1504 GOLU1503
TYPD1508 TYPR1509 TYPI1507
1w1t GOLC1506 GOLP1500 Details
CHQB1513 CHQY1512 GOLX1507
CHQI1513 GOLF1508 CHQM1514 GOLG1509 GOLO1500
1o6i ARGU1520 GOLZ1510 GOLL1513 GOLJ1499 DPRU1519 GOLN1508 GOLH1515 GOLD1512 Details
ARGA1517 GOLG1511 DPRA1516
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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GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
ALJ NAME: CYCLO-(L-ARGININE-L-PROLINE) INHIBITOR
FORMULA: C11 H19 N5 O2
SMILES: NC(N)=NCCCC1NC(=O)C2CCCN2C1=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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