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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1w1t
HYDROLASE HEADER
CRYSTAL STRUCTURE OF S. MARCESCENS CHITINASE B IN COMPLEX WITH THE CYCLIC DIPEPTIDE INHIBITOR CYCLO-(HIS-L-PRO) AT 1.9 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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CHQ Y1512
10R TYR
51R PHE
96R GLY
97R TRP
98R TYR
142R ASP
144R GLU
145R TYR
184R ALA
212R MET
214R TYR
215R ASP
292R TYR
401R MET
403R TRP
CHQ I1513
10A TYR
51A PHE
96A GLY
97A TRP
98A TYR
142A ASP
144A GLU
145A TYR
184A ALA
212A MET
214A TYR
215A ASP
292A TYR
401A MET
403A TRP
CHQ B1513
97R TRP
145R TYR
191R PHE
215R ASP
220R TRP
294R ARG
316R ASP
481A TYR
CHQ M1514
97A TRP
191A PHE
215A ASP
220A TRP
294A ARG
314A GLY
316A ASP
481R TYR
GOL G1509
188A GLY
190A PHE
191A PHE
215A ASP
216A LEU
220A TRP
221A GLU
239A PHE
265A LEU
GOL C1506
190R PHE
220R TRP
221R GLU
239R PHE
464A GLN
479A TRP
480A GLY
481A TYR
GOL P1500
190R PHE
191R PHE
193R SER
194R ARG
479A TRP
480A GLY
481A TYR
482A ILE
483A THR
489A ASP
GOL O1500
190A PHE
191A PHE
221A GLU
239A PHE
464R GLN
479R TRP
480R GLY
481R TYR
GOL X1507
215R ASP
292R TYR
294R ARG
339R ILE
403R TRP
404R HIS
407R GLN
GOL F1508
215A ASP
292A TYR
294A ARG
339A ILE
403A TRP
404A HIS
407A GLN
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).

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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
1w1y TYPJ1508 TYPQ1506 TYPN1507 Details
GOLS1504 GOLU1503
TYPD1508 TYPR1509 TYPI1507
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
CHQ NAME: CYCLO-(L-HISTIDINE-L-PROLINE) INHIBITOR
FORMULA: C11 H14 N4 O2
SMILES: O=C1NC(Cc2[nH]cnc2)C(=O)N3CCCC13
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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