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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1pfk
TRANSFERASE(PHOSPHOTRANSFERASE) HEADER
CRYSTAL STRUCTURE OF THE COMPLEX OF PHOSPHOFRUCTOKINASE FROM ESCHERICHIA COLI WITH ITS REACTION PRODUCTS TITLE
PHOSPHOFRUCTOKINASE 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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ADP U 324
9S SER
10S GLY
11S GLY
41S TYR
71S ALA
72S ARG
73S PHE
74S PRO
76S PHE
77S ARG
82S ARG
102S GLY
103S ASP
104S GLY
105S SER
107S MET
108S GLY
111S ARG
124S GLY
ADP C 324
9A SER
10A GLY
11A GLY
41A TYR
71A ALA
72A ARG
73A PHE
74A PRO
76A PHE
77A ARG
82A ARG
102A GLY
103A ASP
104A GLY
105A SER
107A MET
108A GLY
111A ARG
171A ARG
ADP I 324
9G SER
10G GLY
11G GLY
41G TYR
71G ALA
72G ARG
73G PHE
74G PRO
76G PHE
77G ARG
82G ARG
102G GLY
103G ASP
104G GLY
105G SER
107G MET
108G GLY
111G ARG
124G GLY
ADP O 324
9M SER
10M GLY
11M GLY
41M TYR
71M ALA
72M ARG
73M PHE
74M PRO
76M PHE
77M ARG
82M ARG
102M GLY
103M ASP
104M GLY
105M SER
107M MET
108M GLY
111M ARG
171M ARG
FBP V 323
11S GLY
12S ASP
72S ARG
102S GLY
124S GLY
125S THR
126S ILE
127S ASP
129S ASP
162A ARG
169S MET
170S GLY
171S ARG
222S GLU
223S HIS
243A ARG
249S HIS
252S ARG
FBP D 323
11A GLY
12A ASP
72A ARG
125A THR
126A ILE
127A ASP
129A ASP
162S ARG
169A MET
170A GLY
171A ARG
222A GLU
223A HIS
243S ARG
249A HIS
252A ARG
FBP J 323
11G GLY
12G ASP
72G ARG
102G GLY
124G GLY
125G THR
126G ILE
127G ASP
129G ASP
162M ARG
169G MET
170G GLY
171G ARG
222G GLU
223G HIS
243M ARG
249G HIS
252G ARG
FBP P 323
11M GLY
12M ASP
72M ARG
125M THR
126M ILE
127M ASP
162G ARG
169M MET
170M GLY
171M ARG
222M GLU
223M HIS
243G ARG
249M HIS
252M ARG
ADP B 326
21A ARG
25A ARG
54A ARG
55A TYR
57A VAL
58A SER
59A ASP
60A MET
61A ILE
154G ARG
158G SER
185G GLY
187G GLU
211G LYS
212G GLY
213G LYS
214G LYS
215G HIS
319G TYR
MG F 327
21A ARG
154G ARG
185G GLY
187G GLU
319G TYR
ADP T 326
21S ARG
25S ARG
54S ARG
55S TYR
58S SER
59S ASP
60S MET
61S ILE
154M ARG
158M SER
185M GLY
187M GLU
211M LYS
212M GLY
213M LYS
214M LYS
215M HIS
319M TYR
MG X 327
21S ARG
154M ARG
185M GLY
186M CYS
187M GLU
215M HIS
319M TYR
ADP N 326
21M ARG
25M ARG
54M ARG
55M TYR
57M VAL
58M SER
59M ASP
60M MET
61M ILE
154S ARG
158S SER
185S GLY
187S GLU
211S LYS
212S GLY
213S LYS
214S LYS
215S HIS
319S TYR
MG R 327
21M ARG
154S ARG
185S GLY
187S GLU
215S HIS
319S TYR
ADP H 326
21G ARG
25G ARG
54G ARG
55G TYR
58G SER
59G ASP
60G MET
61G ILE
154A ARG
158A SER
185A GLY
187A GLU
211A LYS
212A GLY
213A LYS
214A LYS
215A HIS
319A TYR
MG L 327
21G ARG
154A ARG
185A GLY
186A CYS
187A GLU
215A HIS
319A TYR
MG E 325
102A GLY
103A ASP
129A ASP
171A ARG
MG Q 325
102M GLY
103M ASP
127M ASP
129M ASP
171M ARG
MG W 325
103S ASP
104S GLY
171S ARG
MG K 325
103G ASP
104G GLY
171G 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.

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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
2pfk 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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ADP NAME: ADENOSINE-5'-DIPHOSPHATE
FORMULA: C10 H15 N5 O10 P2
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O
MG NAME: MAGNESIUM ION
FORMULA: MG1
SMILES: [Mg++]
FBP NAME: FRUCTOSE-1,6-DIPHOSPHATE
FORMULA: C6 H14 O12 P2
SMILES: OC1C(O)C(O)(COP(O)(O)=O)OC1COP(O)(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
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