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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3pyx
OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR HEADER
CRYSTALS STRUCTURE OF ASPARTATE BETA-SEMIALDEHYDE DEHYDROGEN COMPLEX WITH NADP AND 2-AMINOTEREPHTHALATE TITLE
ASPARTATE-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 367
8A VAL
9A GLY
11A THR
12A GLY
13A ALA
14A VAL
15A GLY
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
125A CYS
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 H 367
8G VAL
9G GLY
11G THR
12G GLY
13G ALA
14G VAL
15G GLY
36G ALA
37G SER
39G ARG
40G SER
57G THR
71G SER
72G ALA
73G GLY
74G SER
75G SER
76G THR
79G LYS
80G TYR
94G ASN
95G THR
96G SER
99G ARG
126G PRO
128G CYS
158G SER
159G GLY
160G ALA
161G GLY
162G MET
163G GLY
325G ASN
326G LEU
329G GLY
330G ALA
12T I 371
94G ASN
96G SER
99G ARG
127G ASN
128G CYS
155G GLN
159G GLY
160G ALA
209G ILE
210G ASP
220G GLU
223G LYS
245G ARG
252G HIS
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
2gz1 NAPB_702 Details
NAPD_701
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
12T NAME: not_found
FORMULA: not_found
SMILES: not_found
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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