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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3ol2
SIGNALING PROTEIN HEADER
RECEPTOR-LIGAND STRUCTURE OF HUMAN SEMAPHORIN 4D WITH PLEXIN TITLE
SEMAPHORIN-4D 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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NAG E8001
24O PHE
283O ARG
286O SER
288O LEU
319A ASN
320A VAL
416O LYS
NAG S8001
24A PHE
283A ARG
286A SER
288A LEU
319O ASN
320O VAL
416A LYS
NAG X9000
118O LEU
124O TYR
137O HIS
150O GLU
155O ARG
168O MET
171O GLY
172O GLU
173O LEU
191O ASN
192O SER
193O SER
NAG J9000
118A LEU
124A TYR
137A HIS
150A GLU
155A ARG
168A MET
171A GLY
172A GLU
173A LEU
191A ASN
192A SER
193A SER
NAG U9001
137O HIS
148O LYS
150O GLU
193O SER
NAG G9001
137A HIS
148A LYS
150A GLU
193A SER
NAG L8000
294A ARG
319A ASN
320A VAL
321A GLY
416O LYS
417A ASP
418A VAL
419A ASN
444A ASP
445A ARG
NAG Z8000
294O ARG
319O ASN
320O VAL
321O GLY
416A LYS
417O ASP
418O VAL
419O ASN
444O ASP
445O ARG
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
1olz 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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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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