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 J 510
34J GLN
66J PRO
67J GLY
68J GLY
69J VAL
70J ILE
71J THR
97J SER
98J MET
101J PHE
122J HIS
123J GLN
124J PRO
125J LEU
126J GLY
127J GLY
138J HIS
141J GLU
142J ILE
145J VAL
146J LYS
149J MET
150J ASN
153J MET
168J THR
173I PHE
CMQ H 508
34H GLN
66H PRO
67H GLY
68H GLY
69H VAL
70H ILE
71H THR
97H SER
98H MET
101H PHE
121H ILE
122H HIS
123H GLN
124H PRO
125H LEU
126H GLY
127H GLY
138H HIS
141H GLU
142H ILE
145H VAL
146H LYS
149H MET
150H ASN
153H MET
168H THR
173N PHE
CMQ G 507
34G GLN
66G PRO
67G GLY
68G GLY
69G VAL
70G ILE
71G THR
97G SER
98G MET
101G PHE
118A ARG
122G HIS
123G GLN
124G PRO
125G LEU
126G GLY
127G GLY
129N GLN
138G HIS
141G GLU
142G ILE
145G VAL
146G LYS
149G MET
150G ASN
153G MET
168G THR
173A PHE
CMQ D 504
34D GLN
66D PRO
67D GLY
68D GLY
69D VAL
70D ILE
71D THR
97D SER
98D MET
101D PHE
122D HIS
123D GLN
124D PRO
125D LEU
126D GLY
127D GLY
138D HIS
141D GLU
142D ILE
145D VAL
149D MET
150D ASN
153D MET
168D THR
173E PHE
CMQ K 511
34K GLN
66K PRO
67K GLY
68K GLY
69K VAL
70K ILE
71K THR
97K SER
98K MET
101K PHE
122K HIS
123K GLN
124K PRO
125K LEU
126K GLY
127K GLY
129D GLN
138K HIS
141K GLU
142K ILE
145K VAL
149K MET
150K ASN
153K MET
168K THR
173J PHE
CMQ N 514
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
173M PHE
CMQ L 512
34L GLN
67L GLY
68L GLY
69L VAL
70L ILE
71L THR
97L SER
98L MET
101L PHE
122L HIS
123L GLN
124L PRO
125L LEU
126L GLY
127L GLY
138L HIS
141L GLU
142L ILE
145L VAL
146L LYS
149L MET
150L ASN
153L MET
168L THR
173K PHE
CMQ A 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
173B PHE
CMQ F 506
34F GLN
66F PRO
67F GLY
68F GLY
69F VAL
70F ILE
71F THR
97F SER
98F MET
101F PHE
121F ILE
122F HIS
123F GLN
124F PRO
125F LEU
126F GLY
127F GLY
129M GLN
138F HIS
141F GLU
142F ILE
145F VAL
146F LYS
149F MET
150F ASN
153F MET
168F THR
173G PHE
CMQ E 505
34E GLN
66E PRO
67E GLY
68E GLY
69E VAL
70E ILE
71E THR
97E SER
98E MET
101E PHE
118F ARG
122E HIS
123E GLN
124E PRO
125E LEU
126E GLY
127E GLY
138E HIS
141E GLU
142E ILE
145E VAL
146E LYS
149E MET
150E ASN
153E MET
168E THR
173F PHE
CMQ C 503
34C GLN
66C PRO
67C GLY
68C GLY
69C VAL
70C ILE
71C THR
97C SER
98C MET
101C PHE
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
173D PHE
CMQ I 509
34I GLN
66I PRO
67I GLY
68I GLY
69I VAL
70I ILE
71I THR
97I SER
98I MET
101I PHE
121I ILE
122I HIS
123I GLN
124I PRO
125I LEU
126I GLY
127I GLY
138I HIS
141I GLU
142I ILE
145I VAL
149I MET
150I ASN
153I MET
168I THR
173H PHE
CMQ B 502
34B GLN
67B GLY
68B GLY
69B VAL
70B ILE
71B THR
97B SER
98B MET
101B PHE
121B ILE
122B HIS
123B GLN
124B PRO
125B LEU
126B GLY
127B GLY
129I GLN
138B HIS
141B GLU
142B ILE
145B VAL
146B LYS
149B MET
150B ASN
153B MET
164B ILE
168B THR
173C PHE
CMQ M 513
34M GLN
66M PRO
67M GLY
68M GLY
69M VAL
70M ILE
71M THR
97M SER
98M MET
101M PHE
121M ILE
122M HIS
123M GLN
124M PRO
125M LEU
126M GLY
127M GLY
138M HIS
141M GLU
142M ILE
145M VAL
146M LYS
149M MET
150M ASN
153M MET
164M ILE
168M THR
173L PHE
GOL O3006
70C ILE
71C THR
94D GLN
118D ARG
119D VAL
120D MET
141C GLU
145C VAL
173D PHE
GOL O3007
71H THR
94N GLN
96N ALA
118N ARG
119N VAL
120N MET
141H GLU
145H VAL
173N PHE
GOL O3010
71L THR
94K GLN
96K ALA
118K ARG
119K VAL
120K MET
141L GLU
145L VAL
173K PHE
GOL O3002
71A THR
94B GLN
118B ARG
119B VAL
120B MET
141A GLU
145A VAL
173B PHE
GOL O3009
71F THR
94G GLN
96G ALA
118G ARG
120G MET
141F GLU
145F VAL
173G PHE
GOL O3008
71I THR
94H GLN
118H ARG
119H VAL
120H MET
141I GLU
145I VAL
173H PHE
GOL O3005
71B THR
94C GLN
96C ALA
118C ARG
120C MET
141B GLU
145B VAL
173C PHE
GOL O3011
71M THR
94L GLN
96L ALA
118L ARG
120L MET
141M GLU
145M VAL
173L 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):

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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
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
v6.0
October 2008
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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