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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1hor
INTRAMOLECULAR OXIDOREDUCTASE DEAMINASE HEADER
STRUCTURE AND CATALYTIC MECHANISM OF GLUCOSAMINE 6- PHOSPHATE DEAMINASE FROM ESCHERICHIA COLI AT 2.1 ANGSTROMS RESOLUTION TITLE
GLUCOSAMINE 6-PHOSPHATE DEAMINASE 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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AGP N 268
40M PRO
41M THR
42M GLY
43M GLY
44M THR
45M PRO
70M ASN
71M MET
72M ASP
85M TYR
137M GLY
138M VAL
139M GLY
143M HIS
145M ALA
146M PHE
166M THR
170M ASN
172M ARG
173M PHE
208M LYS
AGP B 268
40A PRO
41A THR
42A GLY
43A GLY
44A THR
45A PRO
71A MET
72A ASP
85A TYR
137A GLY
138A VAL
139A GLY
143A HIS
145A ALA
146A PHE
166A THR
170A ASN
172A ARG
173A PHE
208A LYS
AGP Q 268
40P PRO
41P THR
42P GLY
43P GLY
44P THR
45P PRO
70P ASN
71P MET
72P ASP
85P TYR
137P GLY
138P VAL
139P GLY
143P HIS
144P ILE
145P ALA
146P PHE
166P THR
170P ASN
172P ARG
173P PHE
208P LYS
AGP K 268
40J PRO
41J THR
42J GLY
43J GLY
44J THR
45J PRO
70J ASN
71J MET
72J ASP
85J TYR
137J GLY
138J VAL
139J GLY
143J HIS
145J ALA
146J PHE
166J THR
170J ASN
172J ARG
173J PHE
208J LYS
AGP H 268
40G PRO
41G THR
42G GLY
43G GLY
44G THR
45G PRO
71G MET
72G ASP
85G TYR
137G GLY
138G VAL
139G GLY
143G HIS
145G ALA
146G PHE
166G THR
170G ASN
172G ARG
173G PHE
208G LYS
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
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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
1cd5 Details
other holo-structures
pdb ID Ligand Unique ID
2wu1 FGSK1568 Details
FGSI1568
FGSC1268
FGSG1568
FGSA1268
FGSE1268
1fqo FPCH1268 Details
FPCE1268
F6RK2268
F6RN2268
FPCB1268
F6RQ2268
1fs5 16GE1267 Details
16GB1267
16GH1267
16GO2267
1frz 16GF1267 Details
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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AGP NAME: 2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE
FORMULA: C6 H16 N1 O8 P1
SMILES: NC(CO)C(O)C(O)C(O)COP(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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