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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1vps
VIRAL PROTEIN HEADER
POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE TITLE
POLYOMAVIRUS VP1 PENTAMER 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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SIA F 1
71E GLN
72E TYR
77E ARG
78E GLY
85J ASP
289E ARG
291E THR
293E ASN
296E VAL
298E HIS
SIA G 1
71F GLN
72F TYR
77F ARG
78F GLY
85K ASP
289F ARG
291F THR
293F ASN
296F VAL
298F HIS
SIA Q 1
72P TYR
77P ARG
78P GLY
85A ASP
289P ARG
291P THR
293P ASN
296P VAL
298P HIS
SIA B 1
72A TYR
77A ARG
78A GLY
85U ASP
289A ARG
291A THR
293A ASN
296A VAL
298A HIS
SIA K 1
72J TYR
77J ARG
78J GLY
85O ASP
289J ARG
291J THR
293J ASN
296J VAL
298J HIS
SIA P 1
72O TYR
77O ARG
78O GLY
85Z ASP
289O ARG
291O THR
293O ASN
296O VAL
298O HIS
SIA L 1
72K TYR
77K ARG
78K GLY
85P ASP
289K ARG
291K THR
293K ASN
296K VAL
298K HIS
SIA V 1
72U TYR
77U ARG
78U GLY
85F ASP
289U ARG
291U THR
293U ASN
296U VAL
298U HIS
SIA A 1
72Z TYR
77Z ARG
78Z GLY
85T ASP
289Z ARG
291Z THR
293Z ASN
296Z VAL
298Z HIS
SIA U 1
72T TYR
77T ARG
78T GLY
85E ASP
289T ARG
291T THR
293T ASN
296T VAL
298T HIS
GAL T 2
77P ARG
78P GLY
79P ILE
80P ASN
91P GLY
93P ASN
94P THR
296P VAL
NAG S 3
77P ARG
80P ASN
GAL E 2
77A ARG
78A GLY
79A ILE
80A ASN
91A GLY
93A ASN
94A THR
296A VAL
NAG D 3
77A ARG
80A ASN
GAL I 2
77E ARG
78E GLY
79E ILE
80E ASN
91E GLY
93E ASN
94E THR
296E VAL
NAG H 3
77E ARG
80E ASN
GAL N 2
77J ARG
78J GLY
79J ILE
80J ASN
91J GLY
93J ASN
94J THR
296J VAL
GAL S 2
77O ARG
78O GLY
79O ILE
80O ASN
91O GLY
93O ASN
94O THR
296O VAL
NAG R 3
77O ARG
80O ASN
GAL O 2
77K ARG
78K GLY
79K ILE
80K ASN
91K GLY
93K ASN
94K THR
296K VAL
GAL Y 2
77U ARG
78U GLY
79U ILE
80U ASN
91U GLY
93U ASN
94U THR
296U VAL
NAG X 3
77U ARG
80U ASN
GAL D 2
77Z ARG
78Z GLY
79Z ILE
80Z ASN
91Z GLY
93Z ASN
94Z THR
296Z VAL
NAG C 3
77Z ARG
80Z ASN
GAL J 2
77F ARG
78F GLY
79F ILE
80F ASN
91F GLY
93F ASN
94F THR
296F VAL
NAG I 3
77F ARG
80F ASN
GAL X 2
77T ARG
78T GLY
79T ILE
80T ASN
91T GLY
93T ASN
94T THR
296T VAL
NAG W 3
77T ARG
80T ASN
SIA R 4
80P ASN
81P LEU
82P ALA
83P THR
87P GLU
89P SER
186P LYS
SIA C 4
80A ASN
81A LEU
82A ALA
83A THR
87A GLU
89A SER
91A GLY
186A LYS
SIA G 4
80E ASN
81E LEU
82E ALA
83E THR
87E GLU
89E SER
186E LYS
SIA L 4
80J ASN
81J LEU
82J ALA
83J THR
87J GLU
89J SER
186J LYS
NAG M 3
80J ASN
SIA Q 4
80O ASN
81O LEU
82O ALA
83O THR
87O GLU
89O SER
186O LYS
NAG N 3
80K ASN
SIA M 4
80K ASN
81K LEU
82K ALA
83K THR
87K GLU
89K SER
186K LYS
SIA W 4
80U ASN
81U LEU
83U THR
87U GLU
89U SER
186U LYS
SIA B 4
80Z ASN
81Z LEU
82Z ALA
83Z THR
87Z GLU
89Z SER
91Z GLY
186Z LYS
SIA H 4
80F ASN
81F LEU
82F ALA
83F THR
87F GLU
89F SER
186F LYS
SIA V 4
80T ASN
81T LEU
83T THR
87T GLU
89T SER
186T LYS
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
Help

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).

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apo-structure
pdb ID
1vpn 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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GAL NAME: D-GALACTOSE
FORMULA: C6 H12 O6
SMILES: OCC1OC(O)C(O)C(O)C1O
SIA NAME: O-SIALIC ACID
FORMULA: C11 H19 N1 O9
SMILES: CC(=O)NC1C(O)CC(O)(OC1C(O)C(O)CO)C(O)=O
NAG NAME: N-ACETYL-D-GLUCOSAMINE
FORMULA: C8 H15 N1 O6
SMILES: CC(=O)NC1C(O)OC(CO)C(O)C1O
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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