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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2vhw
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF HOLO L-ALANINE DEHYDROGENASE FROM MYCOBACTERIUM TUBERCULOSIS IN THE OPEN AND CLOSED CONFORMATION TITLE
ALANINE DEHYDROGENASE 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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NAH E1374
75E LYS
96E HIS
118E GLU
127E LEU
130E LEU
131E ALA
133E MET
134E SER
137E ALA
174E ILE
175E GLY
177E GLY
178E THR
179E ALA
180E GLY
197E LEU
198E ASP
199E ILE
200E ASN
203E LYS
220E SER
225E LEU
238E ALA
239E VAL
240E LEU
241E VAL
242E PRO
247E PRO
249E LEU
267E ILE
268E ALA
269E ILE
270E ASP
271E GLN
298E VAL
299E ALA
301E MET
302E PRO
NAH F1374
75F LYS
96F HIS
118F GLU
127F LEU
130F LEU
131F ALA
133F MET
134F SER
137F ALA
174F ILE
175F GLY
177F GLY
178F THR
179F ALA
197F LEU
198F ASP
199F ILE
200F ASN
203F LYS
220F SER
225F LEU
238F ALA
239F VAL
240F LEU
241F VAL
242F PRO
247F PRO
249F LEU
267F ILE
268F ALA
269F ILE
270F ASP
271F GLN
298F VAL
299F ALA
301F MET
302F PRO
NAH C1372
130C LEU
131C ALA
133C MET
134C SER
137C ALA
174C ILE
175C GLY
177C GLY
178C THR
179C ALA
180C GLY
197C LEU
198C ASP
199C ILE
200C ASN
203C LYS
220C SER
225C LEU
238C ALA
239C VAL
240C LEU
241C VAL
242C PRO
247C PRO
249C LEU
267C ILE
268C ALA
269C ILE
270C ASP
271C GLN
298C VAL
299C ALA
301C MET
302C PRO
NAH B1372
130B LEU
131B ALA
133B MET
134B SER
137B ALA
174B ILE
175B GLY
177B GLY
178B THR
179B ALA
197B LEU
198B ASP
199B ILE
200B ASN
203B LYS
220B SER
238B ALA
239B VAL
240B LEU
241B VAL
242B PRO
247B PRO
249B LEU
267B ILE
268B ALA
269B ILE
270B ASP
271B GLN
298B VAL
299B ALA
300B ASN
301B MET
302B PRO
NAH A1373
130A LEU
131A ALA
133A MET
134A SER
137A ALA
174A ILE
175A GLY
177A GLY
178A THR
179A ALA
180A GLY
197A LEU
198A ASP
199A ILE
200A ASN
203A LYS
220A SER
225A LEU
238A ALA
239A VAL
240A LEU
241A VAL
242A PRO
246A ALA
247A PRO
249A LEU
267A ILE
268A ALA
269A ILE
270A ASP
271A GLN
298A VAL
299A ALA
301A MET
302A PRO
NAH D1371
130D LEU
131D ALA
133D MET
134D SER
137D ALA
174D ILE
175D GLY
177D GLY
178D THR
179D ALA
180D GLY
197D LEU
198D ASP
199D ILE
200D ASN
203D LYS
220D SER
225D LEU
238D ALA
239D VAL
240D LEU
241D VAL
247D PRO
249D LEU
267D ILE
268D ALA
269D ILE
270D ASP
271D GLN
298D VAL
299D ALA
301D MET
302D 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:

LigPlot (hosted at the EBI):

» Jmol
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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
2vhy Details
other holo-structures
pdb ID Ligand Unique ID
2vhz NAHC1372 Details
NAHD1372
NAHB1372
NAHF1372
NAHE1372
NAHA1372
2vhx NADF1376 PYRF1375 Details
NADE1375 PYRE1374
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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NAH NAME: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
FORMULA: C21 H27 N7 O14 P2
SMILES: NC(=O)c1ccc[n+](c1)C2OC(COP([O-])(=O)OP(O)(=O)OCC3OC(C(O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
v4.0
May 2008
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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