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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2vhz
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF HOLO L-ALANINE DEHYDROGENASE FROM MYCOBACTERIUM TUBERCULOSIS IN THE 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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NAI D1372
75C LYS
96C HIS
118C GLU
127C LEU
130C LEU
131C ALA
133C MET
134C SER
137C ALA
174C ILE
175C GLY
177C GLY
178C THR
179C ALA
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
300C ASN
301C MET
302C PRO
NAI B1372
75A LYS
96A HIS
118A GLU
127A LEU
130A LEU
131A ALA
133A MET
134A SER
137A ALA
174A ILE
175A GLY
177A GLY
178A THR
179A ALA
180A GLY
198A ASP
199A ILE
200A ASN
203A LYS
220A SER
238A ALA
239A VAL
240A LEU
241A VAL
242A PRO
247A PRO
249A LEU
267A ILE
268A ALA
269A ILE
270A ASP
271A GLN
298A VAL
299A ALA
301A MET
302A PRO
NAI F1372
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
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
300E ASN
301E MET
302E PRO
NAI L1372
75K LYS
96K HIS
118K GLU
127K LEU
130K LEU
131K ALA
133K MET
134K SER
137K ALA
174K ILE
175K GLY
177K GLY
178K THR
179K ALA
180K GLY
197K LEU
198K ASP
199K ILE
200K ASN
203K LYS
220K SER
225K LEU
238K ALA
239K VAL
240K LEU
241K VAL
242K PRO
247K PRO
249K LEU
267K ILE
268K ALA
269K ILE
270K ASP
271K GLN
298K VAL
299K ALA
301K MET
302K PRO
NAI H1372
75G LYS
96G HIS
118G GLU
127G LEU
130G LEU
131G ALA
133G MET
134G SER
137G ALA
174G ILE
175G GLY
177G GLY
178G THR
179G ALA
198G ASP
199G ILE
200G ASN
203G LYS
220G SER
238G ALA
239G VAL
240G LEU
241G VAL
242G PRO
247G PRO
249G LEU
267G ILE
268G ALA
269G ILE
270G ASP
271G GLN
298G VAL
299G ALA
301G MET
302G PRO
NAI J1372
75I LYS
96I HIS
118I GLU
127I LEU
130I LEU
131I ALA
133I MET
134I SER
137I ALA
174I ILE
175I GLY
177I GLY
178I THR
179I ALA
198I ASP
199I ILE
200I ASN
203I LYS
220I SER
225I LEU
238I ALA
239I VAL
240I LEU
241I VAL
242I PRO
246I ALA
247I PRO
249I LEU
267I ILE
268I ALA
269I ILE
270I ASP
271I GLN
298I VAL
299I ALA
300I ASN
301I MET
302I 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):

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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
2vhy Details
other holo-structures
pdb ID Ligand Unique ID
2vhw NAIN1374 Details
NAIJ1371
NAIE1372
NAIG1372
NAIL1374
NAIB1373
2vhx NADO1376 PYRQ1375 Details
NADL1375 PYRM1374
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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NAI NAME: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
FORMULA: C21 H29 N7 O14 P2
SMILES: NC(=O)C1=CN(C=CC1)C2OC(COP(O)(=O)OP(O)(=O)OCC3OC(C(O)C3O)[n]4cnc5c(N)ncnc45)C(O)C2O
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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