university lille north of france LigASite database of binding sites
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LigASite v6.0 (nr25) - non-redundant
LigASite v6.0 (redundant) - redundant
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apo-structureHelp

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

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1hqk
TRANSFERASE HEADER
CRYSTAL STRUCTURE ANALYSIS OF LUMAZINE SYNTHASE FROM AQUIFEX AEOLICUS TITLE
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE COMPND
The XML file of this protein (apo PDB ID 1hqk) is larger than 10MB.
Clicking on any of the "Details" links for the holo-structures will start processing this file to show all HETgroup/Residue contacts.
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be patient while the page loads and do not click "Details" multiple times.
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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20 SER
22 PHE
23 ASN
54 PRO
55 GLY
56 SER
57 TRP
58 GLU
80 VAL
81 LEU
82 ILE
84 GLY
85 ALA
86 THR
88 HIS
89 PHE
92 ILE
112 THR
113 PHE
127 ARG
131 LYS
132 HIS
135 LYS
138 GLU
139 ALA
142 SER
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
1nqw 5YLF3201 27 117 Details
5YLC1201 27 111
5YLI1201 27 116
5YL94201 27 117
5YLG5201 27 113
5YLG2201 27 117
5YLA6201 27 118
5YLD3201 27 115
5YL92201 27 119
5YLI4201 27 119
5YLH1201 27 110
5YLJ3201 27 117
5YL82201 27 114
5YLC2201 27 113
5YLI2201 27 117
5YLE4201 27 113
5YL84201 27 116
5YL85201 27 118
5YL95201 27 113
5YLH4201 27 115
5YLA5201 27 113
5YLJ1201 27 115
5YLB3201 27 108
5YLF2201 27 112
5YLD1201 27 116
5YLB2201 27 119
5YL83201 27 119
5YLH2201 27 112
5YLH5201 27 111
5YLE1201 27 115
5YLF5201 27 111
5YLE3201 27 113
5YLB4201 27 117
5YLH3201 27 117
5YLJ4201 27 120
5YLB5201 27 113
5YLD5201 27 113
5YLI5201 27 113
5YLC5201 27 118
5YLF1201 27 110
5YLE2201 27 114
5YLI3201 27 115
5YLC4201 27 115
5YLJ5201 27 113
5YLA4201 27 114
5YLE5201 27 118
5YLJ2201 27 117
5YLG1201 27 115
5YLF4201 27 115
5YLG3201 27 117
5YLD4201 27 119
5YL81201 27 111
5YLD2201 27 117
5YLG4201 27 120
5YL93201 27 108
5YLB1201 27 115
5YLA3201 27 114
5YLA2201 27 115
5YL91201 27 115
5YLC3201 27 119
1nqv LMZ92201 20 91 Details
LMZG2201 20 89
LMZ82201 20 87
LMZG1201 20 85
LMZD4201 20 85
LMZB5201 20 91
LMZB3201 20 89
LMZA3201 20 88
LMZF4201 20 90
LMZI3201 20 91
LMZ85201 20 90
LMZH1201 20 88
LMZD5201 20 89
LMZJ3201 20 92
LMZE4201 20 87
LMZE1201 20 88
LMZC3201 20 90
LMZI2201 20 85
LMZ93201 20 89
LMZA2201 20 88
LMZG4201 20 90
LMZG3201 20 92
LMZE3201 20 91
LMZC4201 20 87
LMZD3201 20 91
LMZJ4201 20 90
LMZ94201 20 88
LMZE2201 20 88
LMZH5201 20 91
LMZD2201 20 85
LMZB1201 20 90
LMZJ2201 20 89
LMZI4201 20 85
LMZ95201 20 91
LMZA5201 20 87
LMZJ5201 20 91
LMZI5201 20 89
LMZA6201 20 90
LMZD1201 20 88
LMZ83201 20 90
LMZA4201 20 91
LMZH3201 20 88
LMZ84201 20 87
LMZG5201 20 91
LMZB4201 20 88
LMZH2201 20 89
LMZC5201 20 90
LMZF1201 20 88
LMZC2201 20 87
LMZ91201 20 90
LMZF5201 20 91
LMZF2201 20 89
LMZJ1201 20 85
LMZC1201 20 90
LMZF3201 20 88
LMZ81201 20 90
LMZB2201 20 91
LMZI1201 20 88
LMZH4201 20 90
LMZE5201 20 90
1nqx PO4F2251 RLPF2201 32 131 Details
PO4C3251 RLPC3201 32 127
PO484251 RLP84201 32 131
PO4C2251 RLPC2201 32 129
PO4E3251 RLPE3201 32 135
PO4H2251 RLPH2201 32 137
PO491251 RLP91201 32 132
PO4D5251 RLPD5201 32 130
PO4D3251 RLPD3201 32 130
PO4F3251 RLPF3201 32 135
PO4C4251 RLPC4201 32 129
PO4A6251 RLPA6201 32 134
PO4B2251 RLPB2201 32 131
PO4D4251 RLPD4201 32 131
PO4G4251 RLPG4201 32 129
PO4E2251 RLPE2201 32 139
PO4B5251 RLPB5201 32 131
PO493251 RLP93201 32 127
PO495251 RLP95201 32 133
PO4G3251 RLPG3201 32 131
PO4F5251 RLPF5201 32 134
PO4F4251 RLPF4201 32 131
PO4A5251 RLPA5201 32 131
PO4J3251 RLPJ3201 32 134
PO4H5251 RLPH5201 32 136
PO482251 RLP82201 32 133
PO4B4251 RLPB4201 32 127
PO4A3251 RLPA3201 32 131
PO4H4251 RLPH4201 32 129
PO4D1251 RLPD1201 32 132
PO485251 RLP85201 32 130
PO4J1251 RLPJ1201 32 133
PO4I5251 RLPI5201 32 131
PO4I2251 RLPI2201 32 139
PO4H3251 RLPH3201 32 131
PO4E4251 RLPE4201 32 131
PO4J5251 RLPJ5201 32 131
PO4B3251 RLPB3201 32 134
PO4C5251 RLPC5201 32 134
PO4G1251 RLPG1201 32 137
PO4A4251 RLPA4201 32 135
PO4A2251 RLPA2201 32 136
PO483251 RLP83201 32 130
PO4F1251 RLPF1201 32 136
PO4C1251 RLPC1201 32 132
PO4J4251 RLPJ4201 32 127
PO4J2251 RLPJ2201 32 131
PO4I1251 RLPI1201 32 133
PO4D2251 RLPD2201 32 133
PO4E1251 RLPE1201 32 133
PO4I3251 RLPI3201 32 135
PO4G5251 RLPG5201 32 136
PO494251 RLP94201 32 129
PO4H1251 RLPH1201 32 137
PO481251 RLP81201 32 132
PO4I4251 RLPI4201 32 132
PO4B1251 RLPB1201 32 133
PO492251 RLP92201 32 129
PO4E5251 RLPE5201 32 130
PO4G2251 RLPG2201 32 137
1nqu PO4J2251 RDLJ2201 28 124 Details
PO4G3251 RDLG3201 28 121
PO485251 RDL85201 28 126
PO4G1251 RDLG1201 28 126
PO4D1251 RDLD1201 28 124
PO4F3251 RDLF3201 28 121
PO4B4251 RDLB4201 28 126
PO4J4251 RDLJ4201 28 128
PO4D5251 RDLD5201 28 125
PO492251 RDL92201 28 126
PO4I3251 RDLI3201 28 125
PO4G5251 RDLG5201 28 123
PO4I2251 RDLI2201 28 128
PO4G4251 RDLG4201 28 128
PO495251 RDL95201 28 124
PO4I5251 RDLI5201 28 125
PO4D3251 RDLD3201 28 125
PO4H3251 RDLH3201 28 121
PO4B2251 RDLB2201 28 126
PO4J3251 RDLJ3201 28 121
PO481251 RDL81201 28 124
PO4D4251 RDLD4201 28 122
PO4C3251 RDLC3201 28 123
PO4H5251 RDLH5201 28 124
PO4B3251 RDLB3201 28 124
PO4H2251 RDLH2201 28 125
PO4C1251 RDLC1201 28 124
PO493251 RDL93201 28 124
PO4F4251 RDLF4201 28 128
PO4E1251 RDLE1201 28 127
PO4C4251 RDLC4201 28 123
PO4F5251 RDLF5201 28 124
PO4C2251 RDLC2201 28 117
PO4A2251 RDLA2201 28 127
PO4I4251 RDLI4201 28 122
PO4G2251 RDLG2201 28 124
PO4H4251 RDLH4201 28 128
PO4E4251 RDLE4201 28 122
PO4E3251 RDLE3201 28 128
PO482251 RDL82201 28 117
PO484251 RDL84201 28 123
PO491251 RDL91201 28 125
PO4E5251 RDLE5201 28 120
PO4A3251 RDLA3201 28 123
PO4I1251 RDLI1201 28 124
PO4A4251 RDLA4201 28 128
PO4A6251 RDLA6201 28 120
PO4C5251 RDLC5201 28 126
PO4D2251 RDLD2201 28 128
PO494251 RDL94201 28 126
PO4J1251 RDLJ1201 28 126
PO4A5251 RDLA5201 28 122
PO4H1251 RDLH1201 28 127
PO4F1251 RDLF1201 28 127
PO4F2251 RDLF2201 28 125
PO483251 RDL83201 28 123
PO4E2251 RDLE2201 28 123
PO4B1251 RDLB1201 28 125
PO4J5251 RDLJ5201 28 123
PO4B5251 RDLB5201 28 124
v6.0
October 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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