university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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apo-structureHelp

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

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1vdq
HYDROLASE HEADER
THE CRYSTAL STRUCTURE OF THE ORTHORHOMBIC FORM OF HEN EGG WHITE LYSOZYME AT 1.5 ANGSTROMS RESOLUTION TITLE
LYSOZYME C 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 LYS
2 VAL
20 TYR
34 PHE
35 GLU
40 THR
41 GLN
44 ASN
45 ARG
46 ASN
47 THR
48 ASP
50 SER
52 ASP
56 LEU
57 GLN
58 ILE
59 ASN
61 ARG
62 TRP
63 TRP
73 ARG
75 LEU
76 CYS
77 ASN
78 ILE
84 LEU
85 SER
86 SER
89 THR
90 ALA
93 ASN
94 CYS
97 LYS
98 ILE
101 ASP
102 GLY
103 ASN
104 GLY
106 ASN
107 ALA
108 TRP
109 VAL
110 ALA
112 ARG
114 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:

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» 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
2fbb NO3F_158 NO3L_158 _NAR_132 NO3T_150 NO3S_150 17 70 Details
1jj0 SUCA2380 23 70 Details
1sfb NAGA_201 NAGA_202 NAGA_203 NAGA_205 NAGA_204 71 190 Details
2znx 1PGB_243 17 89 Details
1PGA_243 17 92
1hew NAGA_201 NAGA_202 NAGA_203 43 116 Details
1uih NAGA_501 NAGA_502 NAGA_503 43 112 Details
1sf7 NAGA_201 NAGA_202 NAGA_203 NAGA_204 57 167 Details
3sp3 SUCA_130 23 74 Details
1sf4 NAGA_201 NAGA_202 29 104 Details
1sf6 NAGA_201 NAGA_202 NAGA_203 NAGA_204 57 172 Details
1uc0 GALA_130 GOLA_132 NAGA_131 30 98 Details
2znw 1PGB_243 17 102 Details
1PGA_243 17 103
1lzc NAGA_130 NAGA_132 NAGA_131 43 97 Details
1sfg NAGA_201 NAGA_202 NAGA_203 NAGA_205 NAGA_204 71 195 Details
1at5 NAGA_132 NAGA_131 29 74 Details
NAGA_130 NAGA_132 NAGA_131 43 84
2hub EDOA1001 EPEA2001 19 75 Details
1lzb NAGA_132 NAGA_131 28 76 Details
NAGA_130 NAGA_132 NAGA_131 43 109
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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