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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1pze
OXIDOREDUCTASE HEADER
T.GONDII LDH1 APO FORM TITLE
LACTATE DEHYDROGENASE 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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26 ILE
27 GLY
28 SER
29 GLY
30 MET
31 ILE
32 GLY
52 TYR
53 ASP
54 VAL
55 VAL
58 MET
85 TYR
97 THR
98 ALA
99 GLY
100 LEU
101 THR
107 TRP
109 ARG
112 LEU
116 ASN
118 LYS
119 ILE
122 GLU
123 ILE
138 VAL
139 THR
140 ASN
142 LEU
163 MET
164 ALA
167 LEU
171 ARG
195 HIS
236 GLY
240 VAL
244 GLY
245 SER
246 ALA
247 TYR
250 PRO
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
1pzh NADH_703 OXLI_704 50 193 Details
NADK_707 OXLL_708 50 195
NADE_705 OXLF_706 50 185
NADB_701 OXLC_702 50 189
1pzg A3DC_601 SO4B_602 49 187 Details
A3DL_607 SO4K_608 49 190
A3DF_605 SO4E_606 49 192
A3DI_603 SO4H_604 49 190
1pzf A3DB_401 OXLC_402 50 183 Details
A3DK_407 OXLL_408 50 190
A3DH_403 OXLI_404 50 195
A3DE_405 OXLF_406 50 186
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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