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

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

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2c3s
HYDROLASE HEADER
STRUCTURE OF SARS COV MAIN PROTEINASE AT 1.9 A (PH6.5) TITLE
SARS COV 3C-LIKE PROTEINASE COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

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

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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1 SER
24 THR
25 THR
26 THR
27 LEU
39 PRO
41 HIS
42 VAL
44 CYS
45 THR
46 ALA
49 MET
50 LEU
52 PRO
54 TYR
119 ASN
140 PHE
141 LEU
142 ASN
143 GLY
144 SER
145 CYS
163 HIS
164 HIS
165 MET
166 GLU
167 LEU
168 PRO
172 HIS
187 ASP
188 ARG
189 GLN
190 THR
191 ALA
192 GLN
305 PHE
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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
2zu4 ZU3B_501 44 165 Details
ZU3A_501 44 165
2gz7 D3FB_307 28 98 Details
D3FD_307 28 95
3sn8 S89D_307 32 117 Details
S89B_307 32 119
2hob 3IHA1145 49 182 Details
2a5i AZPD_307 46 153 Details
AZPB_307 46 159
3iwm 3IHJ1001 49 184 Details
3IHF1001 49 173
3IHH1001 49 175
3IHN1001 49 173
3IHL1001 49 191
3IHP1001 49 173
3IHD1001 49 197
3IHB1001 49 192
2gz8 F3FB_307 25 103 Details
F3FD_307 25 104
2gx4 NOLD2001 43 166 Details
NOLB2001 43 164
2z3c 0E2A_503 44 147 Details
0E2C_503 44 144
2zu5 ZU5B2001 45 163 Details
ZU5A2001 45 159
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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