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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2fzs
HYDROLASE HEADER
CRYSTAL STRUCTURE OF E. COLI CLPP WITH A PEPTIDE CHLOROMETHYL KETONE COVALENTLY BOUND AT THE ACTIVE SITE TITLE
ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 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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CMQ O 505
34N GLN
66N PRO
67N GLY
68N GLY
69N VAL
70N ILE
71N THR
97N SER
98N MET
101N PHE
122N HIS
123N GLN
124N PRO
125N LEU
126N GLY
127N GLY
138N HIS
141N GLU
142N ILE
145N VAL
146N LYS
149N MET
150N ASN
153N MET
168N THR
CMQ A 504
34Z GLN
66Z PRO
67Z GLY
68Z GLY
69Z VAL
70Z ILE
71Z THR
97Z SER
98Z MET
101Z PHE
122Z HIS
123Z GLN
124Z PRO
125Z LEU
126Z GLY
127Z GLY
138Z HIS
141Z GLU
142Z ILE
145Z VAL
149Z MET
150Z ASN
153Z MET
168Z THR
173N PHE
CMQ Y 514
34X GLN
66X PRO
67X GLY
68X GLY
69X VAL
70X ILE
71X THR
97X SER
98X MET
101X PHE
122X HIS
123X GLN
124X PRO
125X LEU
126X GLY
127X GLY
138X HIS
141X GLU
142X ILE
145X VAL
146X LYS
149X MET
150X ASN
153X MET
168X THR
CMQ B 501
34A GLN
66A PRO
67A GLY
68A GLY
69A VAL
70A ILE
71A THR
97A SER
98A MET
101A PHE
121A ILE
122A HIS
123A GLN
124A PRO
125A LEU
126A GLY
127A GLY
138A HIS
141A GLU
142A ILE
145A VAL
149A MET
150A ASN
153A MET
168A THR
CMQ D 508
34C GLN
66C PRO
67C GLY
68C GLY
69C VAL
70C ILE
71C THR
97C SER
98C MET
101C PHE
121C ILE
122C HIS
123C GLN
124C PRO
125C LEU
126C GLY
127C GLY
138C HIS
141C GLU
142C ILE
145C VAL
146C LYS
149C MET
150C ASN
153C MET
168C THR
173X PHE
CMQ N 511
34M GLN
66M PRO
67M GLY
68M GLY
69M VAL
70M ILE
71M THR
97M SER
98M MET
101M PHE
122M HIS
123M GLN
124M PRO
125M LEU
126M GLY
127M GLY
129Z GLN
138M HIS
141M GLU
142M ILE
145M VAL
149M MET
150M ASN
153M MET
168M THR
GOL C3002
71A THR
141A GLU
145A VAL
GOL Z3007
71C THR
94X GLN
96X ALA
118X ARG
119X VAL
120X MET
141C GLU
145C VAL
173X PHE
GOL H3008
94C GLN
118C ARG
119C VAL
120C MET
173C PHE
GOL W3006
94Z GLN
118Z ARG
119Z VAL
120Z MET
173Z PHE
GOL O3010
94M GLN
96M ALA
118M ARG
119M VAL
120M MET
173M PHE
CMQ K 507
118A ARG
129X GLN
173A PHE
CMQ G 509
173C PHE
CMQ V 503
173Z PHE
CMQ R 512
173M PHE
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
1tyf 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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CMQ NAME: N~2~-[(BENZYLOXY)CARBONYL]-N-[(1S,2S)-2-HYDROXY-1-(4-HYDROXYBENZYL)PROPYL]-L-LEUCINAMIDE
FORMULA: C24 H32 N2 O5
SMILES: CC(C)CC(NC(=O)OCc1ccccc1)C(=O)NC(Cc2ccc(O)cc2)C(C)O
GOL NAME: GLYCEROL
FORMULA: C3 H8 O3
SMILES: OCC(O)CO
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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