university lille north of france LigASite database of binding sites
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LigASite v7.0 (nr25) - non-redundant
LigASite v7.0 (redundant) - redundant
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apo-structureHelp

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

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1kf5
HYDROLASE HEADER
ATOMIC RESOLUTION STRUCTURE OF RNASE A AT PH 7.1 TITLE
PANCREATIC RIBONUCLEASE 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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2 GLU
3 THR
4 ALA
7 LYS
8 PHE
11 GLN
12 HIS
39 ARG
41 LYS
42 PRO
43 VAL
44 ASN
45 THR
65 CYS
66 LYS
67 ASN
69 GLN
71 ASN
72 CYS
83 ASP
85 ARG
104 LYS
107 ILE
109 ALA
111 GLU
118 VAL
119 HIS
120 PHE
121 ASP
122 ALA
123 SER
124 VAL
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:

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» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
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
1rca CGP__150 CGP__160 PO4__170 28 84 Details
1afk PAPA_125 31 97 Details
PAPB_125 31 98
1rnc CPG__161 SO4__151 29 91 Details
1rpf C3PB_125 21 73 Details
C3PA_125 21 73
1afl ATRB_125 31 96 Details
ATRA_125 31 96
1o0n U3PC1201 21 72 Details
U3PC1101 21 74
1rnn FMTF_131 __CC_200 24 86 Details
FMTD_131 __CB_200 24 83
1o0h ADPC1125 27 83 Details
ADPC1126 27 77
1z6d IMPA_919 IMPA_921 IMPA_920 69 161 Details
1w4p UM3A1125 20 76 Details
1u1b PAXA_901 51 141 Details
1rpg CPA__126 37 111 Details
1ruv UVC__125 21 76 Details
1w4q UMFA1125 21 79 Details
1rob C2P__126 21 70 Details
1rnm SO4D_125 SO4F_125 SO4F_127 __CC_200 __CB_200 SO4D_127 62 228 Details
8rsa ADTA_125 20 72 Details
ADTB_125 20 71
1w4o UA3A1125 21 77 Details
1rnd DCG__126 SO4__125 28 85 Details
1o0m U2PC1101 21 71 Details
U2PC1201 21 78
1jn4 139A_901 42 122 Details
1z6s AMPA1101 23 74 Details
1o0f A3PC1401 27 77 Details
A3PC1301 27 70
1eow SO4__125 U2G__130 25 96 Details
2qca DGPA_200 DGPA_300 46 126 Details
v7.0
March 2009		 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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