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)
1ake
TRANSFERASE(PHOSPHOTRANSFERASE) HEADER
STRUCTURE OF THE COMPLEX BETWEEN ADENYLATE KINASE FROM ESCHERICHIA COLI AND THE INHIBITOR AP5A REFINED AT 1.9 ANGSTROMS RESOLUTION: A MODEL FOR A CATALYTIC TRANSITION STATE TITLE
ADENYLATE KINASE 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)
AP5 A 215
9A PRO
10A GLY
11A ALA
12A GLY
13A LYS
14A GLY
15A THR
16A GLN
31A THR
32A GLY
35A LEU
36A ARG
53A MET
56A GLY
57A LYS
58A LEU
59A VAL
64A VAL
84A ASP
85A GLY
86A PHE
88A ARG
92A GLN
119A ARG
120A ILE
123A ARG
132A VAL
133A TYR
134A HIS
137A PHE
138A ASN
156A ARG
158A ASP
167A ARG
198A GLY
199A THR
200A LYS
201A PRO
202A VAL
205A VAL
AP5 B 215
9B PRO
10B GLY
11B ALA
12B GLY
13B LYS
14B GLY
15B THR
16B GLN
31B THR
32B GLY
35B LEU
36B ARG
53B MET
56B GLY
57B LYS
58B LEU
59B VAL
64B VAL
84B ASP
85B GLY
86B PHE
88B ARG
92B GLN
119B ARG
120B ILE
123B ARG
132B VAL
133B TYR
134B HIS
137B PHE
138B ASN
156B ARG
158B ASP
167B ARG
198B GLY
199B THR
200B LYS
201B PRO
202B VAL
205B VAL
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
4ake Details
other holo-structures
pdb ID Ligand Unique ID
3hpq AP5A_215 Details
AP5B_215
1ank AMPB_215 ANPB_216 Details
AMPA_215 ANPA_216
2eck AMPB_215 Details
AMPA_215
ADPB_216
ADPA_216
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)
AP5 NAME: BIS(ADENOSINE)-5'-PENTAPHOSPHATE
FORMULA: C20 H29 N10 O22 P5
SMILES: Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(=O)OP(O)(=O)OP(O)(=O)OCC4OC(C(O)C4O)[n]5cnc6c(N)ncnc56)C(O)C3O
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: 0.1439 seconds