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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1hka
TRANSFERASE HEADER
6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE TITLE
6-HYDROXYMETHYL-7,8-DIHYDROPTERIN 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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6 ALA
7 ILE
8 GLY
10 ASN
42 THR
43 PRO
44 PRO
45 LEU
46 GLY
47 PRO
50 GLN
53 TYR
55 ASN
56 ALA
70 LEU
73 THR
74 GLN
77 GLU
82 ARG
84 ARG
85 LYS
86 ALA
87 GLU
88 ARG
89 TRP
90 GLY
91 PRO
92 ARG
93 THR
94 LEU
95 ASP
96 LEU
97 ASP
98 ILE
109 GLU
110 ARG
111 LEU
112 THR
113 VAL
115 HIS
116 TYR
117 ASP
120 ASN
121 ARG
123 PHE
124 MET
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
1rb0 HH2A_181 22 86 Details
3ude ACTA_191 J1BA_171 47 172 Details
1ex8 A4PA_171 _MGA_161 49 169 Details
1eqm ADPA_171 _MGA_161 28 91 Details
3ud5 EDOA_192 J1AA_171 45 166 Details
EDOA_191 EDOA_192 J1AA_171 49 193
3udv ACTA_191 J1CA_171 48 183 Details
1rao AMPA_171 23 76 Details
HH2A_181 22 71
1dy3 87YJ_201 _MGI_202 _MGH_203 ATPG_200 56 235 Details
87YE_201 _MGD_202 ATPB_200 _MGC_203 56 245
3ip0 ACTJ_194 _MGD_161 HHRF_181 APCE_171 _MGC_162 51 205 Details
ACTT_194 _MGM_162 _MGN_161 APCO_171 HHRP_181 51 205
1q0n ACTR_164 _MGM_161 APCL_171 PH2O_181 _MGN_162 51 198 Details
ACTI_164 _MGD_161 PH2F_181 APCC_171 _MGE_162 51 202
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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