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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1w1y
HYDROLASE HEADER
CRYSTAL STRUCTURE OF S. MARCESCENS CHITINASE B IN COMPLEX WITH THE CYCLIC DIPEPTIDE INHIBITOR CYCLO-(L-TYR-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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TYP Q1506
10M TYR
51M PHE
96M GLY
97M TRP
98M TYR
142M ASP
144M GLU
184M ALA
212M MET
214M TYR
215M ASP
292M TYR
294M ARG
316M ASP
339M ILE
401M MET
403M TRP
TYP I1507
10A TYR
51A PHE
96A GLY
97A TRP
98A TYR
142A ASP
144A GLU
184A ALA
212A MET
214A TYR
215A ASP
292A TYR
294A ARG
316A ASP
339A ILE
401A MET
403A TRP
TYP N1507
12M PHE
51M PHE
95M GLY
96M GLY
97M TRP
98M TYR
99M TYR
316M ASP
317M PRO
318M TYR
334M ASP
336M ASP
339M ILE
403M TRP
404M HIS
407M GLN
TYP D1508
12A PHE
51A PHE
95A GLY
96A GLY
97A TRP
98A TYR
99A TYR
316A ASP
317A PRO
318A TYR
334A ASP
336A ASP
339A ILE
403A TRP
404A HIS
407A GLN
TYP J1508
97M TRP
101M ASN
103M LEU
191M PHE
215M ASP
220M TRP
294M ARG
314M GLY
316M ASP
461A THR
481A TYR
483A THR
TYP R1509
97A TRP
101A ASN
103A LEU
144A GLU
191A PHE
212A MET
215A ASP
220A TRP
294A ARG
314A GLY
316A ASP
461M THR
481M TYR
483M THR
GOL S1504
188M GLY
190M PHE
191M PHE
215M ASP
216M LEU
217M ALA
220M TRP
221M GLU
239M PHE
265M LEU
GOL U1503
190M PHE
221M GLU
239M 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:

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
1e15 Details
other holo-structures
pdb ID Ligand Unique ID
1w1v GOLE1500 GOLK1506 Details
ALJT1520 GOLJ1517 GOLF1509 GOLR1516
GOLD1500 GOLZ1507 GOLB1512
ALJK1513 GOLZ1507 GOLB1512 GOLH1510 GOLX1511 GOLY1508
1e6r AMIL1502 NAAK1501 NAAJ1500 Details
AMIF1501 NAAE1500 NAAD1499
1w1p GIOL1518 GOLI1510 GOLK1514 Details
GOLH1508 GOLV1512
1ur8 GDLI2502 NAGH2501 Details
GDLP2502 SO4L1510 NAGO2501
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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TYP NAME: CYCLO-(L-TYROSINE-L-PROLINE) INHIBITOR
FORMULA: C14 H16 N2 O3
SMILES: Oc1ccc(CC2NC(=O)C3CCCN3C2=O)cc1
GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
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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