university lille north of france LigASite database of binding sites
holo-structureHelp

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

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1rao
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E. COLI HPPK WITH AMP AND 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE AT 1.56 ANGSTROM RESOLUTION TITLE
2-AMINO-4-HYDROXY-6- COMPND
Illustration of Binding SiteHelp

Figure showing the binding site residues. Ligands are displayed as CPK. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR). Ligands do not appear on the picture when PISA fails to apply symmetry operations to ligand coordinates.

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HETgroup - Residue ContactsHelp

List of binding site residues detected in this holo-structure.

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

The binding residues in this holo structure are listed for each ligand independently, following the ligand's unique ID.

Note that since PISA files are used whenever available, chain identifiers may differ from those in original PDB files.

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HH2 A 181
8A GLY
42A THR
43A PRO
44A PRO
45A LEU
53A TYR
55A ASN
95A ASP
97A ASP
115A HIS
116A TYR
121A ARG
123A PHE
AMP A 171
70A LEU
74A GLN
77A GLU
92A ARG
95A ASP
96A LEU
97A ASP
98A ILE
109A GLU
110A ARG
111A LEU
112A THR
113A VAL
115A HIS
116A TYR
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:

LigPlot (hosted at the EBI):

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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Hide table of related structures
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List of related structure, containing both the apo-structure and other holo-structures.

Column 1 gives the PDB ID and column 2 the unique ID of the ligands (holo-structures only).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
1hka Details
other holo-structures
pdb ID Ligand Unique ID
1rb0 HH2A_181 Details
3ude ACTA_191 J1BA_171 Details
1ex8 A4PA_171 _MGA_161 Details
1eqm ADPA_171 _MGA_161 Details
3ud5 EDOA_192 J1AA_171 Details
EDOA_191 EDOA_192 J1AA_171
3udv ACTA_191 J1CA_171 Details
1dy3 87YJ_201 _MGI_202 _MGH_203 ATPG_200 Details
87YE_201 _MGD_202 ATPB_200 _MGC_203
3ip0 ACTJ_194 _MGD_161 HHRF_181 APCE_171 _MGC_162 Details
ACTT_194 _MGM_162 _MGN_161 APCO_171 HHRP_181
1q0n ACTR_164 _MGM_161 APCL_171 PH2O_181 _MGN_162 Details
ACTI_164 _MGD_161 PH2F_181 APCC_171 _MGE_162
Ligand ListHelp

Ligands present in this holo structure.

Column 1 shows the ligand HET code
Column 2 shows the name, chemical formula and (non-stereo) SMILES string.

Data in column 2 appears as 'not_found' when it is not present in the file 'pdb2smiles.xml' from www.rcsb.org.

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AMP NAME: ADENOSINE MONOPHOSPHATE
FORMULA: C10 H14 N5 O7 P1
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(O)=O)C(O)C3O
HH2 NAME: 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE
FORMULA: C7 H9 N5 O8 P2
SMILES: NC1=Nc2ncc(COP(O)(=O)OP(O)(O)=O)nc2C(=O)N1
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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