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)
3b4y
OXIDOREDUCTASE HEADER
FGD1 (RV0407) FROM MYCOBACTERIUM TUBERCULOSIS TITLE
PROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE 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)
F42 E 338
9D LYS
13D GLU
38D SER
39D ASP
40D HIS
73D SER
74D VAL
76D THR
80D ARG
106D GLY
107D THR
108D GLY
109D GLU
112D ASN
113D GLU
125D PHE
128D ARG
175D ALA
176D ALA
177D GLY
178D GLY
179D PRO
180D ALA
181D VAL
193D ILE
194D CYS
195D THR
198D LYS
230D GLU
256D ALA
260D HIS
F42 B 338
9A LYS
13A GLU
38A SER
39A ASP
40A HIS
73A SER
74A VAL
76A THR
80A ARG
106A GLY
107A THR
108A GLY
109A GLU
112A ASN
125A PHE
128A ARG
175A ALA
176A ALA
177A GLY
178A GLY
179A PRO
180A ALA
181A VAL
193A ILE
194A CYS
195A THR
198A LYS
230A GLU
256A ALA
260A HIS
FLC F 337
13D GLU
40D HIS
44D TRP
109D GLU
177D GLY
195D THR
198D LYS
230D GLU
232D LYS
252D LEU
259D LYS
260D HIS
283D ARG
FLC C 337
13A GLU
40A HIS
44A TRP
109A GLU
177A GLY
195A THR
198A LYS
230A GLU
232A LYS
252A LEU
259A LYS
260A HIS
283A ARG
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
3c8n 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)
F42 NAME: COENZYME F420
FORMULA: C29 H35 N5 O18 P1
SMILES: CC(OP(O)(=O)OCC(O)C(O)C(O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13)C(=O)NC(CCC(=O)NC(CCC(O)=O)C(O)=O)C(O)=O
FLC NAME: CITRATE ANION
FORMULA: C6 H5 O7
SMILES: OC(CC([O-])=O)(CC([O-])=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: 0.0696 seconds