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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2var
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS 2-KETO-3- DEOXYGLUCONATE KINASE COMPLEXED WITH 2-KETO-3- DEOXYGLUCONATE TITLE
FRUCTOKINASE 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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KDF E1314
9E GLU
11E LEU
34E GLY
35E SER
90E TYR
104E LEU
106E TYR
108E ARG
137E ILE
166E ARG
169E LEU
254E THR
255E GLY
258E ASP
294E ASP
KDG C1313
9C GLU
11C LEU
34C GLY
35C SER
90C TYR
104C LEU
106C TYR
108C ARG
137C ILE
166C ARG
169C LEU
254C THR
255C GLY
258C ASP
KDF C1314
9C GLU
11C LEU
34C GLY
35C SER
38C ASN
90C TYR
104C LEU
106C TYR
108C ARG
137C ILE
166C ARG
254C THR
258C ASP
294C ASP
KDF D1314
9D GLU
11D LEU
34D GLY
35D SER
36D GLU
38D ASN
90D TYR
104D LEU
106D TYR
108D ARG
137D ILE
166D ARG
254D THR
255D GLY
258D ASP
294D ASP
KDF F1314
9F GLU
11F LEU
34F GLY
35F SER
38F ASN
90F TYR
104F LEU
106F TYR
108F ARG
137F ILE
166F ARG
254F THR
258F ASP
294F ASP
KDG F1313
9F GLU
11F LEU
34F GLY
35F SER
90F TYR
104F LEU
106F TYR
108F ARG
137F ILE
166F ARG
169F LEU
254F THR
255F GLY
258F ASP
KDF B1314
9B GLU
11B LEU
34B GLY
35B SER
90B TYR
104B LEU
106B TYR
108B ARG
137B ILE
166B ARG
169B LEU
254B THR
255B GLY
258B ASP
294B ASP
KDF A1314
9A GLU
11A LEU
34A GLY
35A SER
36A GLU
38A ASN
90A TYR
104A LEU
106A TYR
108A ARG
137A ILE
166A ARG
254A THR
255A GLY
258A ASP
294A ASP
KDG E1313
11E LEU
34E GLY
35E SER
38E ASN
104E LEU
106E TYR
108E ARG
137E ILE
164E ASN
166E ARG
254E THR
255E GLY
258E ASP
294E ASP
KDG D1313
11D LEU
34D GLY
35D SER
38D ASN
90D TYR
104D LEU
106D TYR
108D ARG
137D ILE
166D ARG
169D LEU
254D THR
255D GLY
258D ASP
294D ASP
KDG B1313
11B LEU
34B GLY
35B SER
38B ASN
104B LEU
106B TYR
108B ARG
137B ILE
164B ASN
166B ARG
254B THR
255B GLY
258B ASP
294B ASP
KDG A1313
11A LEU
34A GLY
35A SER
38A ASN
90A TYR
104A LEU
106A TYR
108A ARG
137A ILE
166A ARG
169A LEU
254A THR
255A GLY
258A ASP
294A ASP
AMP E1316
100E MET
101E LYS
226E LYS
227E LEU
228E GLY
229E SER
231E GLY
232E ALA
245E ALA
250E VAL
253E PRO
256E ALA
257E GLY
260E MET
282E ILE
285E SER
289E ILE
ANP E1315
100E MET
101E LYS
162E ASP
164E ASN
166E ARG
195E ASP
226E LYS
228E GLY
229E SER
231E GLY
245E ALA
246E TYR
247E LYS
248E VAL
250E VAL
253E PRO
254E THR
255E GLY
256E ALA
257E GLY
258E ASP
260E MET
282E ILE
285E SER
286E THR
289E ILE
AMP C1316
100C MET
101C LYS
195C ASP
226C LYS
228C GLY
229C SER
231C GLY
245C ALA
246C TYR
247C LYS
248C VAL
250C VAL
253C PRO
256C ALA
260C MET
282C ILE
285C SER
286C THR
289C ILE
ANP C1315
100C MET
101C LYS
162C ASP
164C ASN
166C ARG
195C ASP
226C LYS
227C LEU
228C GLY
231C GLY
232C ALA
245C ALA
246C TYR
248C VAL
250C VAL
253C PRO
254C THR
255C GLY
256C ALA
257C GLY
258C ASP
260C MET
282C ILE
285C SER
286C THR
289C ILE
AMP D1316
100D MET
101D LYS
195D ASP
226D LYS
227D LEU
228D GLY
229D SER
231D GLY
232D ALA
245D ALA
246D TYR
250D VAL
253D PRO
256D ALA
257D GLY
260D MET
282D ILE
285D SER
286D THR
289D ILE
ANP D1315
100D MET
101D LYS
162D ASP
164D ASN
166D ARG
195D ASP
226D LYS
228D GLY
229D SER
231D GLY
245D ALA
246D TYR
247D LYS
248D VAL
250D VAL
253D PRO
254D THR
255D GLY
256D ALA
257D GLY
258D ASP
260D MET
282D ILE
285D SER
286D THR
289D ILE
AMP F1316
100F MET
101F LYS
195F ASP
226F LYS
228F GLY
229F SER
231F GLY
245F ALA
246F TYR
247F LYS
248F VAL
250F VAL
253F PRO
256F ALA
260F MET
282F ILE
285F SER
286F THR
289F ILE
ANP F1315
100F MET
101F LYS
162F ASP
164F ASN
166F ARG
195F ASP
226F LYS
227F LEU
228F GLY
231F GLY
232F ALA
245F ALA
246F TYR
248F VAL
250F VAL
253F PRO
254F THR
255F GLY
256F ALA
257F GLY
258F ASP
260F MET
282F ILE
285F SER
286F THR
289F ILE
AMP B1316
100B MET
101B LYS
226B LYS
227B LEU
228B GLY
229B SER
231B GLY
232B ALA
245B ALA
250B VAL
253B PRO
256B ALA
257B GLY
260B MET
282B ILE
285B SER
289B ILE
ANP B1315
100B MET
101B LYS
162B ASP
164B ASN
166B ARG
195B ASP
226B LYS
228B GLY
229B SER
231B GLY
245B ALA
246B TYR
247B LYS
248B VAL
250B VAL
253B PRO
254B THR
255B GLY
256B ALA
257B GLY
258B ASP
260B MET
282B ILE
285B SER
286B THR
289B ILE
AMP A1316
100A MET
101A LYS
195A ASP
226A LYS
227A LEU
228A GLY
229A SER
231A GLY
232A ALA
245A ALA
246A TYR
250A VAL
253A PRO
256A ALA
257A GLY
260A MET
282A ILE
285A SER
286A THR
289A ILE
ANP A1315
100A MET
101A LYS
162A ASP
164A ASN
166A ARG
195A ASP
226A LYS
228A GLY
229A SER
231A GLY
245A ALA
246A TYR
247A LYS
248A VAL
250A VAL
253A PRO
254A THR
255A GLY
256A ALA
257A GLY
258A ASP
260A MET
282A ILE
285A SER
286A THR
289A ILE
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):

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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
2v78 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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AMP NAME: ADENOSINE MONOPHOSPHATE
FORMULA: C10 H14 N5 O7 P1
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(O)=O)C(O)C3O
KDF NAME: not_found
FORMULA: not_found
SMILES: not_found
ANP NAME: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
FORMULA: C10 H17 N6 O12 P3
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)NP(O)(O)=O)C(O)C3O
KDG NAME: 2-KETO-3-DEOXYGLUCONATE
FORMULA: C6 H10 O6
SMILES: OCC(O)C(O)CC(=O)C(O)=O
v6.0
October 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
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