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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2gz1
OXIDOREDUCTASE HEADER
STRUCTURE OF ASPARTATE SEMIALDEHYDE DEHYDROGENASE (ASADH) FROM STREPTOCOCCUS PNEUMONIAE COMPLEXED WITH NADP TITLE
ASPARTATE BETA-SEMIALDEHYDE 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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NAP B 702
8A VAL
9A GLY
11A THR
12A GLY
13A ALA
14A VAL
36A ALA
37A SER
39A ARG
40A SER
57A THR
71A SER
72A ALA
73A GLY
74A SER
76A THR
79A LYS
80A TYR
94A ASN
95A THR
96A SER
99A ARG
126A PRO
127A ASN
128A CYS
158A SER
159A GLY
160A ALA
161A GLY
162A MET
163A GLY
325A ASN
326A LEU
329A GLY
330A ALA
NAP D 701
8C VAL
9C GLY
11C THR
12C GLY
13C ALA
14C VAL
15C GLY
36C ALA
37C SER
39C ARG
40C SER
56C GLU
57C THR
71C SER
72C ALA
73C GLY
74C SER
76C THR
80C TYR
94C ASN
95C THR
96C SER
99C ARG
126C PRO
127C ASN
128C CYS
158C SER
159C GLY
160C ALA
161C GLY
162C MET
163C GLY
325C ASN
326C LEU
329C GLY
330C ALA
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
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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
2gyy Details
other holo-structures
pdb ID Ligand Unique ID
2gz3 AS2A_400 NAPB_367 Details
AS2C_400 NAPD_367
3pwk 25AC_367 Details
25AL_367
3q11 NAPG_367 Details
NAPB_367
3pws A2PE_368 Details
A2PC_369
2gz2 A2PD_501 Details
A2PB_502
3pzb 2RAA_367 NAPB_368 Details
2RAF_367 NAPG_368
3pyx NAPB_367 Details
12TI_371 NAPH_367
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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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
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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