university lille north of france LigASite database of binding sites
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LigASite v7.0 (nr25) - non-redundant
LigASite v7.0 (redundant) - redundant
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apo-structureHelp

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

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1dhn
PTERINE BINDING HEADER
1.65 ANGSTROM RESOLUTION STRUCTURE OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AUREUS TITLE
7,8-DIHYDRONEOPTERIN ALDOLASE 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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5 ILE
13 TYR
14 GLY
15 TYR
16 HIS
17 GLY
18 ALA
19 LEU
22 GLU
24 GLU
25 ILE
39 LEU
48 VAL
51 THR
52 VAL
53 HIS
54 TYR
55 GLY
56 GLU
58 PHE
59 GLU
62 LYS
65 MET
66 GLU
67 GLY
68 LYS
69 ALA
71 ASN
72 LEU
73 LEU
74 GLU
100 LYS
103 PRO
104 PRO
105 ILE
106 PRO
107 GLY
108 HIS
114 ILE
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
1rsd PSBO1001 36 139 Details
PSBJ1001 36 138
PSBL1001 36 138
PSBI1001 36 139
PSBN1001 36 139
PSBK1001 36 138
PSBM1001 36 139
PSBP1001 36 138
1rs4 45PJ1001 29 124 Details
45PM1001 29 131
45PK1001 29 126
45PO1001 29 123
45PL1001 29 124
45PN1001 29 131
45PI1001 29 123
45PP1001 29 126
1u68 NPRL1001 18 87 Details
NPRK1001 18 83
NPRJ1001 18 87
NPRP1001 18 83
NPRO1001 18 84
NPRI1001 18 84
NPRN1001 18 85
NPRM1001 18 85
2nm3 MPUE_131 18 89 Details
MPUB_131 18 88
MPUA_131 18 86
MPUC_131 18 91
MPUD_131 18 88
MPUF_131 18 89
MPUG_131 18 86
MPUH_131 18 91
2nm2 NEUE_222 18 78 Details
NEUD_422 18 83
NEUC_322 18 93
NEUH_322 18 94
NEUF_122 18 92
NEUB_222 18 81
NEUG_422 18 85
NEUA_122 18 95
1rsi 977L1001 15 76 Details
977K1001 15 73
977O1001 15 74
977N1001 15 77
977M1001 15 77
977I1001 15 74
977P1001 15 73
977J1001 15 76
1rs2 209I1001 14 72 Details
209O1001 14 72
1rri A45O1001 20 81 Details
A45N1001 20 82
A45P1001 20 80
A45L1001 20 78
A45M1001 20 82
A45J1001 20 78
A45I1001 20 81
A45K1001 20 80
v7.0
March 2009		 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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