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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1fwk
TRANSFERASE HEADER
CRYSTAL STRUCTURE OF HOMOSERINE KINASE COMPLEXED WITH ADP TITLE
HOMOSERINE 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.

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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 D 700
34C ASP
54C ASN
55C ILE
56C PRO
61C LYS
62C ASN
63C VAL
64C ALA
85C ILE
87C LYS
90C LYS
91C ALA
92C GLY
93C SER
94C GLY
95C LEU
96C GLY
97C SER
98C SER
99C ALA
101C SER
130C GLU
133C SER
134C SER
141C ASN
183C THR
261C SER
ADP B 600
50A VAL
54A ASN
55A ILE
56A PRO
61A LYS
62A ASN
63A VAL
85A ILE
87A LYS
90A LYS
91A ALA
92A GLY
93A SER
94A GLY
95A LEU
96A GLY
97A SER
98A SER
99A ALA
101A SER
130A GLU
133A SER
134A SER
141A ASN
181A ILE
182A ASN
183A THR
ADP H 900
50G VAL
54G ASN
55G ILE
56G PRO
61G LYS
62G ASN
63G VAL
85G ILE
87G LYS
90G LYS
91G ALA
92G GLY
93G SER
94G GLY
95G LEU
96G GLY
97G SER
98G SER
99G ALA
101G SER
130G GLU
133G SER
134G SER
141G ASN
183G THR
261G SER
ADP F 800
54E ASN
55E ILE
56E PRO
61E LYS
62E ASN
63E VAL
85E ILE
87E LYS
90E LYS
91E ALA
92E GLY
93E SER
94E GLY
95E LEU
96E GLY
97E SER
98E SER
99E ALA
101E SER
130E GLU
133E SER
134E SER
141E ASN
181E ILE
182E ASN
183E THR
MG I 597
98G SER
130G GLU
133G SER
134G SER
183G THR
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).

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apo-structure
pdb ID
1fwl Details
other holo-structures
pdb ID Ligand Unique ID
1h74 ILEC_500 SAPD_400 _MGE_600 Details
ADPG_400
ADPB_400
ILEH_500 SAPI_400
1h72 ANPF1301 HSEG1300 Details
ANPB1301 HSEC1300
1h73 ANPB_418 THRA_401 Details
ANPD_418 THRC_401
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++]
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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