university lille north of france LigASite database of binding sites
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

(click anywhere in this window to remove it)
1sow
OXIDOREDUCTASE HEADER
T. GONDII BRADYZOITE-SPECIFIC LDH (LDH2) IN COMPLEX WITH NAD AND OXALATE TITLE
L-LACTATE 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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
NAD K 501
26J ILE
27J GLY
29J GLY
30J MET
31J ILE
32J GLY
52J PHE
53J ASP
54J VAL
55J VAL
58J MET
85J TYR
97J THR
98J ALA
99J GLY
100J LEU
101J THR
107J TRP
112J LEU
116J ASN
119J ILE
122J GLU
123J VAL
138J VAL
139J THR
140J ASN
142J LEU
163J MET
164J ALA
167J LEU
195J HIS
244J GLY
245J SER
246J ALA
250J PRO
NAD H 401
26G ILE
27G GLY
29G GLY
30G MET
31G ILE
32G GLY
52G PHE
53G ASP
54G VAL
55G VAL
58G MET
85G TYR
97G THR
98G ALA
99G GLY
100G LEU
101G THR
107G TRP
112G LEU
116G ASN
119G ILE
122G GLU
123G VAL
138G VAL
139G THR
140G ASN
142G LEU
163G MET
164G ALA
167G LEU
195G HIS
244G GLY
245G SER
246G ALA
250G PRO
NAD E 501
26D ILE
27D GLY
29D GLY
30D MET
31D ILE
32D GLY
52D PHE
53D ASP
54D VAL
55D VAL
58D MET
85D TYR
97D THR
98D ALA
99D GLY
100D LEU
101D THR
107D TRP
112D LEU
116D ASN
119D ILE
122D GLU
123D VAL
138D VAL
139D THR
140D ASN
142D LEU
163D MET
164D ALA
167D LEU
195D HIS
244D GLY
245D SER
246D ALA
250D PRO
NAD B 401
26A ILE
27A GLY
29A GLY
30A MET
31A ILE
32A GLY
52A PHE
53A ASP
54A VAL
55A VAL
58A MET
85A TYR
97A THR
98A ALA
99A GLY
100A LEU
101A THR
107A TRP
112A LEU
116A ASN
119A ILE
122A GLU
123A VAL
138A VAL
139A THR
140A ASN
142A LEU
163A MET
164A ALA
167A LEU
195A HIS
244A GLY
245A SER
246A ALA
250A PRO
OXL L 502
107J TRP
109J ARG
140J ASN
167J LEU
171J ARG
195J HIS
236J GLY
245J SER
246J ALA
OXL I 402
107G TRP
109G ARG
140G ASN
167G LEU
171G ARG
195G HIS
236G GLY
245G SER
246G ALA
OXL F 502
107D TRP
109D ARG
140D ASN
167D LEU
171D ARG
195D HIS
236D GLY
245D SER
246D ALA
OXL C 402
107A TRP
109A ARG
140A ASN
167A LEU
171A ARG
195A HIS
236A GLY
245A SER
246A 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.

(click anywhere in this window to remove it)

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.

(click anywhere in this window to remove it)
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.

(click anywhere in this window to remove it)
apo-structure
pdb ID
1sov 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.

(click anywhere in this window to remove it)
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
OXL NAME: OXALATE ION
FORMULA: C2 O4
SMILES: [O-]C(=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
Script execution time: 0.1864 seconds