university lille north of france LigASite database of binding sites
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LigASite v3.0 (nr25) - non-redundant
LigASite v3.0 (redundant) - redundant
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apo-structureHelp

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

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1e15
HYDROLASE HEADER
CHITINASE B FROM SERRATIA MARCESCENS TITLE
CHITINASE B COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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10 TYR
12 PHE
14 PRO
51 PHE
95 GLY
96 GLY
97 TRP
98 TYR
99 TYR
101 ASN
103 LEU
142 ASP
144 GLU
145 TYR
184 ALA
186 ALA
187 GLY
188 GLY
190 PHE
191 PHE
193 SER
194 ARG
212 MET
214 TYR
215 ASP
216 LEU
217 ALA
220 TRP
221 GLU
239 PHE
265 LEU
292 TYR
294 ARG
314 GLY
316 ASP
317 PRO
318 TYR
333 ARG
334 ASP
336 ASP
339 ILE
401 MET
403 TRP
404 HIS
407 GLN
461 THR
464 GLN
479 TRP
480 GLY
481 TYR
482 ILE
483 THR
484 SER
489 ASP
490 SER
491 ALA
1517 ARG
1520 ARG
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:

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» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
1w1t CHQA1513 CHQA1514 GOLA1500 GOLA1509 GOLA1508 52 207 Details
GOLB1500 GOLB1506 12 77
CHQB1512 GOLB1507 CHQB1513 40 154
1o6i ARGB1520 DPRB1519 GOLB1515 GOLB1508 GOLB1512 GOLB1510 GOLB1513 GOLA1499 54 282 Details
GOLA1498 GOLA1512 GOLB1500 18 89
ARGA1517 DPRA1516 GOLA1511 24 118
1w1p GIOA1518 GOLA1514 GOLA1510 23 94 Details
1w1y TYPA1507 TYPA1509 TYPA1508 57 229 Details
TYPB1506 TYPB1507 TYPB1508 57 242
GOLB1503 GOLB1504 12 70
1e6r AMIB1502 NAAB1500 NAAB1501 43 148 Details
AMIA1501 NAAA1500 NAAA1499 43 146
1w1v ALJB1513 GOLB1507 GOLB1508 GOLB1512 GOLB1500 GOLB1511 GOLB1510 54 248 Details
ALJA1520 GOLA1517 GOLA1509 GOLA1516 36 158
GOLA1500 GOLA1506 12 74
1ur8 GDLB2502 SO4B1510 NAGB2501 34 120 Details
GDLA2502 NAGA2501 29 106
v3.0
January 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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