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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2gz8
HYDROLASE HEADER
STRUCTURE-BASED DRUG DESIGN AND STRUCTURAL BIOLOGY STUDY OF NOVEL NONPEPTIDE INHIBITORS OF SARS-COV MAIN PROTEASE TITLE
REPLICASE POLYPROTEIN 1AB 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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F3F B 307
1C SER
25A THR
26A THR
27A LEU
41A HIS
140A PHE
141A LEU
142A ASN
143A GLY
144A SER
145A CYS
163A HIS
165A MET
166A GLU
167A LEU
168A PRO
188A ARG
189A GLN
190A THR
192A GLN
F3F D 307
25C THR
26C THR
27C LEU
41C HIS
140C PHE
141C LEU
142C ASN
143C GLY
144C SER
145C CYS
163C HIS
165C MET
166C GLU
167C LEU
168C PRO
188C ARG
189C GLN
190C THR
192C GLN
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).

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

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apo-structure
pdb ID
2bx3 Details
other holo-structures
pdb ID Ligand Unique ID
2zu4 ZU3B_501 Details
ZU3A_501
2gz7 D3FB_307 Details
D3FD_307
3sn8 S89D_307 Details
S89B_307
2hob 3IHA1145 Details
2a5i AZPD_307 Details
AZPB_307
3iwm 3IHJ1001 Details
3IHF1001
3IHH1001
3IHN1001
3IHL1001
3IHP1001
3IHD1001
3IHB1001
2gx4 NOLD2001 Details
NOLB2001
2z3c 0E2A_503 Details
0E2C_503
2zu5 ZU5B2001 Details
ZU5A2001
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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F3F NAME: not_found
FORMULA: not_found
SMILES: not_found
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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