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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3gpo
VIRAL PROTEIN HEADER
CRYSTAL STRUCTURE OF MACRO DOMAIN OF CHIKUNGUNYA VIRUS IN COMPLEX WITH ADP-RIBOSE TITLE
NON-STRUCTURAL PROTEIN 3 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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APR D 161
10D ASP
11D ILE
22D ALA
23D ALA
24D ASN
30D GLY
31D ASP
32D GLY
33D VAL
34D CYS
36D ALA
70D GLY
107D PRO
108D LEU
109D LEU
110D SER
111D THR
112D GLY
113D VAL
114D TYR
142D TYR
143D CYS
144D ARG
148D TRP
APR A 161
10A ASP
11A ILE
22A ALA
23A ALA
24A ASN
30A GLY
31A ASP
32A GLY
33A VAL
34A CYS
36A ALA
70A GLY
107A PRO
108A LEU
109A LEU
110A SER
111A THR
112A GLY
113A VAL
114A TYR
142A TYR
143A CYS
144A ARG
145A ASP
148A TRP
APR B 161
10B ASP
11B ILE
22B ALA
23B ALA
24B ASN
30B GLY
31B ASP
32B GLY
33B VAL
34B CYS
36B ALA
70B GLY
107B PRO
108B LEU
109B LEU
110B SER
111B THR
112B GLY
113B VAL
114B TYR
142B TYR
143B CYS
144B ARG
145B ASP
148B TRP
APR C 161
10C ASP
11C ILE
22C ALA
23C ALA
24C ASN
26C ARG
30C GLY
31C ASP
32C GLY
33C VAL
34C CYS
36C ALA
70C GLY
107C PRO
108C LEU
109C LEU
110C SER
111C THR
112C GLY
113C VAL
114C TYR
142C TYR
143C CYS
144C ARG
145C ASP
148C TRP
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
3gpg Details
other holo-structures
pdb ID Ligand Unique ID
none
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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APR NAME: ADENOSINE-5-DIPHOSPHORIBOSE
FORMULA: C15 H23 N5 O14 P2
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OCC4OC(O)C(O)C4O)C(O)C3O
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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