university lille north of france LigASite database of binding sites
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:

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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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 PSBJ1001 36 139 Details
PSBL1001 36 138
PSBN1001 36 138
PSBH1001 36 139
PSBB1001 36 139
PSBD1001 36 138
PSBF1001 36 138
PSBP1001 36 139
1rs4 45PJ1001 29 123 Details
45PL1001 29 124
45PF1001 29 124
45PN1001 29 126
45PH1001 29 131
45PB1001 29 123
45PD1001 29 126
45PP1001 29 131
2dhn PH2N_122 14 73 Details
PH2P_122 14 73
PH2J_122 14 74
PH2D_122 14 73
PH2B_122 14 74
PH2H_122 14 73
1u68 NPRL1001 18 87 Details
NPRJ1001 18 84
NPRP1001 18 85
NPRH1001 18 85
NPRD1001 18 83
NPRF1001 18 87
NPRB1001 18 84
NPRN1001 18 83
2nm3 MPUK_131 18 89 Details
MPUE_131 18 91
MPUN_131 18 86
MPUB_131 18 86
MPUT_131 18 91
MPUW_131 18 89
MPUH_131 18 88
MPUQ_131 18 88
2nm2 NEUF_122 18 92 Details
NEUN_322 18 94
NEUP_422 18 83
NEUB_122 18 95
NEUD_222 18 78
NEUH_222 18 81
NEUL_422 18 85
NEUJ_322 18 93
1rsi 977L1001 15 74 Details
977N1001 15 77
977B1001 15 73
977P1001 15 76
977J1001 15 73
977H1001 15 76
977F1001 15 74
977D1001 15 77
1rs2 209L1001 14 72 Details
209F1001 14 72
1rri A45N1001 20 80 Details
A45H1001 20 82
A45P1001 20 82
A45L1001 20 78
A45B1001 20 81
A45J1001 20 81
A45F1001 20 78
A45D1001 20 80
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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