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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3o03
OXIDOREDUCTASE HEADER
QUATERNARY COMPLEX STRUCTURE OF GLUCONATE 5-DEHYDROGENASE FR STREPTOCOCCUS SUIS TYPE 2 TITLE
DEHYDROGENASE WITH DIFFERENT SPECIFICITIES 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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NAP G 273
21E GLY
23E SER
24E TYR
25E GLY
26E ILE
27E GLY
44E ASN
45E ASP
46E ILE
50E LEU
70E CYS
71E ASP
72E VAL
73E THR
97E ASN
98E ASN
99E ALA
100E GLY
101E ILE
102E ILE
121E ILE
148E ILE
149E CYS
163E TYR
167E LYS
193E PRO
194E GLY
195E TYR
196E ILE
198E THR
NAP K 273
21I GLY
23I SER
24I TYR
25I GLY
26I ILE
27I GLY
44I ASN
45I ASP
46I ILE
50I LEU
70I CYS
71I ASP
72I VAL
97I ASN
98I ASN
99I ALA
100I GLY
101I ILE
102I ILE
121I ILE
122I ASP
148I ILE
149I CYS
163I TYR
167I LYS
193I PRO
194I GLY
195I TYR
196I ILE
198I THR
NAP O 273
21M GLY
23M SER
24M TYR
25M GLY
26M ILE
27M GLY
44M ASN
45M ASP
46M ILE
50M LEU
70M CYS
71M ASP
72M VAL
73M THR
97M ASN
98M ASN
99M ALA
100M GLY
101M ILE
102M ILE
121M ILE
148M ILE
149M CYS
163M TYR
167M LYS
193M PRO
194M GLY
195M TYR
196M ILE
198M THR
NAP C 273
21A GLY
23A SER
24A TYR
25A GLY
26A ILE
27A GLY
44A ASN
45A ASP
46A ILE
50A LEU
70A CYS
71A ASP
72A VAL
97A ASN
98A ASN
99A ALA
100A GLY
101A ILE
102A ILE
121A ILE
122A ASP
148A ILE
149A CYS
163A TYR
167A LYS
193A PRO
194A GLY
195A TYR
196A ILE
198A THR
GCO H 274
102E ILE
104E ARG
150E SER
151E MET
152E MET
157E ARG
160E VAL
163E TYR
194E GLY
195E TYR
216E PHE
265M ILE
268M GLN
GCO L 274
102I ILE
104I ARG
150I SER
151I MET
152I MET
157I ARG
160I VAL
163I TYR
194I GLY
195I TYR
216I PHE
265A ILE
268A GLN
GCO P 274
102M ILE
104M ARG
150M SER
151M MET
152M MET
157M ARG
160M VAL
163M TYR
194M GLY
195M TYR
216M PHE
265E ILE
268E GLN
GCO D 274
102A ILE
104A ARG
150A SER
151A MET
152A MET
157A ARG
160A VAL
163A TYR
194A GLY
195A TYR
216A PHE
265I ILE
268I GLN
CA F 272
150E SER
151E MET
193E PRO
194E GLY
CA J 272
150I SER
151I MET
193I PRO
194I GLY
CA N 272
150M SER
151M MET
193M PRO
194M GLY
CA B 272
150A SER
151A MET
193A PRO
194A GLY
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).

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apo-structure
pdb ID
3cxr Details
other holo-structures
pdb ID Ligand Unique ID
none
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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GCO NAME: GLUCONIC ACID
FORMULA: C6 H12 O7
SMILES: OCC(O)C(O)C(O)C(O)C(O)=O
NAP NAME: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
FORMULA: C21 H28 N7 O17 P3
SMILES: NC(=O)c1ccc[n+](c1)C2OC(COP([O-])(=O)OP(O)(=O)OCC3OC(C(OP(O)(O)=O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
CA NAME: CALCIUM ION
FORMULA: CA1
SMILES: [Ca++]
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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