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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3d4p
OXIDOREDUCTASE HEADER
CRYSTAL STRUCTURE OF LACTATE DEHYDROGENASE FROM STAPHYLOCOCCUS AUREUS COMPLEXED WITH NAD AND PYRUVATE TITLE
L-LACTATE DEHYDROGENASE 1 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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NAD B 318
12A ILE
13A GLY
14A ASN
15A GLY
16A ALA
17A VAL
18A GLY
37A ILE
38A ASP
39A LEU
40A ASP
43A LYS
69A TYR
81A CYS
82A ALA
83A GLY
84A ALA
85A ALA
86A GLN
95A LEU
99A ASN
102A ILE
105A SER
106A ILE
122A ALA
123A THR
124A ASN
126A VAL
147A SER
148A GLY
150A ILE
151A LEU
179A HIS
231A ALA
232A THR
236A VAL
NAD H 318
12G ILE
13G GLY
14G ASN
15G GLY
16G ALA
17G VAL
18G GLY
37G ILE
38G ASP
39G LEU
40G ASP
43G LYS
69G TYR
81G CYS
82G ALA
83G GLY
84G ALA
85G ALA
86G GLN
95G LEU
99G ASN
102G ILE
105G SER
106G ILE
122G ALA
123G THR
124G ASN
126G VAL
147G SER
148G GLY
150G ILE
151G LEU
179G HIS
231G ALA
232G THR
236G VAL
NAD K 318
12J ILE
13J GLY
14J ASN
15J GLY
16J ALA
17J VAL
18J GLY
37J ILE
38J ASP
39J LEU
40J ASP
43J LYS
69J TYR
81J CYS
82J ALA
83J GLY
84J ALA
85J ALA
86J GLN
95J LEU
99J ASN
102J ILE
105J SER
106J ILE
122J ALA
123J THR
124J ASN
126J VAL
147J SER
148J GLY
150J ILE
151J LEU
179J HIS
231J ALA
232J THR
236J VAL
NAD E 318
12D ILE
13D GLY
14D ASN
15D GLY
16D ALA
17D VAL
18D GLY
37D ILE
38D ASP
39D LEU
40D ASP
43D LYS
69D TYR
81D CYS
82D ALA
83D GLY
84D ALA
85D ALA
86D GLN
95D LEU
99D ASN
102D ILE
105D SER
106D ILE
122D ALA
123D THR
124D ASN
126D VAL
147D SER
148D GLY
150D ILE
151D LEU
179D HIS
231D ALA
232D THR
236D VAL
PYR C 319
124A ASN
151A LEU
155A ARG
179A HIS
222A ALA
226A ILE
232A THR
PYR I 319
124G ASN
151G LEU
155G ARG
179G HIS
222G ALA
226G ILE
232G THR
PYR L 319
124J ASN
151J LEU
155J ARG
179J HIS
222J ALA
226J ILE
232J THR
PYR F 319
124D ASN
151D LEU
155D ARG
179D HIS
222D ALA
226D ILE
232D THR
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
3d0o 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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NAD 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
PYR NAME: PYRUVIC ACID
FORMULA: C3 H4 O3
SMILES: CC(=O)C(O)=O
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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