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)
1pzh
OXIDOREDUCTASE HEADER
T.GONDII LDH1 TERNARY COMPLEX WITH NAD AND OXALATE TITLE
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 E 701
26A ILE
27A GLY
29A GLY
30A MET
31A ILE
32A GLY
52A TYR
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
118A LYS
119A ILE
122A GLU
123A ILE
138A VAL
139A THR
140A ASN
142A LEU
163A MET
164A ALA
167A LEU
195A HIS
244A GLY
245A SER
246A ALA
250A PRO
NAD E 707
26D ILE
27D GLY
28D SER
29D GLY
30D MET
31D ILE
32D GLY
52D TYR
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 ILE
138D VAL
139D THR
140D ASN
142D LEU
163D MET
164D ALA
167D LEU
195D HIS
245D SER
246D ALA
247D TYR
250D PRO
NAD E 703
26B ILE
27B GLY
28B SER
29B GLY
30B MET
31B ILE
32B GLY
52B TYR
53B ASP
54B VAL
55B VAL
58B MET
85B TYR
97B THR
98B ALA
99B GLY
100B LEU
101B THR
107B TRP
112B LEU
116B ASN
119B ILE
122B GLU
123B ILE
138B VAL
139B THR
140B ASN
142B LEU
163B MET
164B ALA
167B LEU
195B HIS
244B GLY
245B SER
246B ALA
250B PRO
NAD E 705
26C ILE
27C GLY
28C SER
29C GLY
30C MET
31C ILE
32C GLY
52C TYR
53C ASP
54C VAL
55C VAL
58C MET
85C TYR
97C THR
98C ALA
99C GLY
100C LEU
101C THR
107C TRP
112C LEU
116C ASN
119C ILE
122C GLU
123C ILE
138C VAL
139C THR
140C ASN
142C LEU
163C MET
164C ALA
167C LEU
195C HIS
244C GLY
245C SER
246C ALA
250C PRO
OXL E 702
107A TRP
109A ARG
140A ASN
167A LEU
171A ARG
195A HIS
236A GLY
245A SER
246A ALA
OXL E 708
107D TRP
109D ARG
140D ASN
167D LEU
171D ARG
195D HIS
236D GLY
245D SER
246D ALA
OXL E 704
107B TRP
109B ARG
140B ASN
167B LEU
171B ARG
195B HIS
236B GLY
245B SER
246B ALA
OXL E 706
107C TRP
109C ARG
140C ASN
167C LEU
171C ARG
195C HIS
236C GLY
245C SER
246C 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):

» Jmol
» Jmol
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
1pze Details
other holo-structures
pdb ID Ligand Unique ID
1pzg A3DE_601 SO4E_602 Details
A3DE_603 SO4E_604
A3DE_607 SO4E_608
A3DE_605 SO4E_606
1pzf A3DE_407 OXLE_408 Details
A3DE_403 OXLE_404
A3DE_401 OXLE_402
A3DE_405 OXLE_406
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
v3.0
January 2008
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: 0.4945 seconds