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 R1314
9P GLU
11P LEU
34P GLY
35P SER
90P TYR
104P LEU
106P TYR
108P ARG
137P ILE
166P ARG
169P LEU
254P THR
255P GLY
258P ASP
294P ASP
KDF C1314
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
KDF M1314
9K GLU
11K LEU
34K GLY
35K SER
36K GLU
38K ASN
90K TYR
104K LEU
106K TYR
108K ARG
137K ILE
166K ARG
254K THR
255K GLY
258K ASP
294K ASP
KDF W1314
9U GLU
11U LEU
34U GLY
35U SER
38U ASN
90U TYR
104U LEU
106U TYR
108U ARG
137U ILE
166U ARG
254U THR
258U ASP
294U ASP
KDG V1313
9U GLU
11U LEU
34U GLY
35U SER
90U TYR
104U LEU
106U TYR
108U ARG
137U ILE
166U ARG
169U LEU
254U THR
255U GLY
258U ASP
KDG A1313
9Z GLU
11Z LEU
34Z GLY
35Z SER
90Z TYR
104Z LEU
106Z TYR
108Z ARG
137Z ILE
166Z ARG
169Z LEU
254Z THR
255Z GLY
258Z ASP
KDF B1314
9Z GLU
11Z LEU
34Z GLY
35Z SER
38Z ASN
90Z TYR
104Z LEU
106Z TYR
108Z ARG
137Z ILE
166Z ARG
254Z THR
258Z ASP
294Z ASP
KDF H1314
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
294F ASP
KDG Q1313
11P LEU
34P GLY
35P SER
38P ASN
104P LEU
106P TYR
108P ARG
137P ILE
164P ASN
166P ARG
254P THR
255P GLY
258P ASP
294P ASP
KDG B1313
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
KDG L1313
11K LEU
34K GLY
35K SER
38K ASN
90K TYR
104K LEU
106K TYR
108K ARG
137K ILE
166K ARG
169K LEU
254K THR
255K GLY
258K ASP
294K ASP
KDG G1313
11F LEU
34F GLY
35F SER
38F ASN
104F LEU
106F TYR
108F ARG
137F ILE
164F ASN
166F ARG
254F THR
255F GLY
258F ASP
294F ASP
AMP T1316
100P MET
101P LYS
226P LYS
227P LEU
228P GLY
229P SER
231P GLY
232P ALA
245P ALA
250P VAL
253P PRO
256P ALA
257P GLY
260P MET
282P ILE
285P SER
289P ILE
ANP S1315
100P MET
101P LYS
162P ASP
164P ASN
166P ARG
195P ASP
226P LYS
228P GLY
229P SER
231P GLY
245P ALA
246P TYR
247P LYS
248P VAL
250P VAL
253P PRO
254P THR
255P GLY
256P ALA
257P GLY
258P ASP
260P MET
282P ILE
285P SER
286P THR
289P ILE
AMP E1316
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 D1315
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
AMP O1316
100K MET
101K LYS
195K ASP
226K LYS
227K LEU
228K GLY
229K SER
231K GLY
232K ALA
245K ALA
246K TYR
250K VAL
253K PRO
256K ALA
257K GLY
260K MET
282K ILE
285K SER
286K THR
289K ILE
ANP N1315
100K MET
101K LYS
162K ASP
164K ASN
166K ARG
195K ASP
226K LYS
228K GLY
229K SER
231K GLY
245K ALA
246K TYR
247K LYS
248K VAL
250K VAL
253K PRO
254K THR
255K GLY
256K ALA
257K GLY
258K ASP
260K MET
282K ILE
285K SER
286K THR
289K ILE
AMP Y1316
100U MET
101U LYS
195U ASP
226U LYS
228U GLY
229U SER
231U GLY
245U ALA
246U TYR
247U LYS
248U VAL
250U VAL
253U PRO
256U ALA
260U MET
282U ILE
285U SER
286U THR
289U ILE
ANP X1315
100U MET
101U LYS
162U ASP
164U ASN
166U ARG
195U ASP
226U LYS
227U LEU
228U GLY
231U GLY
232U ALA
245U ALA
246U TYR
248U VAL
250U VAL
253U PRO
254U THR
255U GLY
256U ALA
257U GLY
258U ASP
260U MET
282U ILE
285U SER
286U THR
289U ILE
AMP D1316
100Z MET
101Z LYS
195Z ASP
226Z LYS
228Z GLY
229Z SER
231Z GLY
245Z ALA
246Z TYR
247Z LYS
248Z VAL
250Z VAL
253Z PRO
256Z ALA
260Z MET
282Z ILE
285Z SER
286Z THR
289Z ILE
ANP C1315
100Z MET
101Z LYS
162Z ASP
164Z ASN
166Z ARG
195Z ASP
226Z LYS
227Z LEU
228Z GLY
231Z GLY
232Z ALA
245Z ALA
246Z TYR
248Z VAL
250Z VAL
253Z PRO
254Z THR
255Z GLY
256Z ALA
257Z GLY
258Z ASP
260Z MET
282Z ILE
285Z SER
286Z THR
289Z ILE
AMP J1316
100F MET
101F LYS
226F LYS
227F LEU
228F GLY
229F SER
231F GLY
232F ALA
245F ALA
250F VAL
253F PRO
256F ALA
257F GLY
260F MET
282F ILE
285F SER
289F ILE
ANP I1315
100F MET
101F LYS
162F ASP
164F ASN
166F ARG
195F ASP
226F LYS
228F GLY
229F SER
231F GLY
245F ALA
246F TYR
247F LYS
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
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
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
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
KDF NAME: not_found
FORMULA: not_found
SMILES: not_found
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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