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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1r3q
LYASE HEADER
UROPORPHYRINOGEN DECARBOXYLASE IN COMPLEX WITH COPROPORPHYRINOGEN-I TITLE
UROPORPHYRINOGEN DECARBOXYLASE 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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1CP B 901
36A MET
37A ARG
38A GLN
39A ALA
40A GLY
41A ARG
46A PHE
50A ARG
55A PHE
82A ILE
83A ILE
84A PHE
85A SER
86A ASP
87A ILE
88A LEU
100A MET
104A LYS
105A GLY
106A PRO
154A PHE
164A TYR
170A GLY
217A PHE
219A SER
220A HIS
261A PHE
263A LYS
339A HIS
1CP E 901
36D MET
37D ARG
38D GLN
39D ALA
40D GLY
41D ARG
46D PHE
50D ARG
55D PHE
82D ILE
83D ILE
84D PHE
85D SER
86D ASP
87D ILE
88D LEU
100D MET
104D LYS
105D GLY
106D PRO
154D PHE
164D TYR
170D GLY
217D PHE
219D SER
220D HIS
261D PHE
263D LYS
339D HIS
CO2 C5001
37A ARG
CO2 F5001
37D ARG
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).

Clicking the blue 'Hide table of related structures' button removes the entire table.

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apo-structure
pdb ID
3gvq Details
other holo-structures
pdb ID Ligand Unique ID
1r3y CP3B_867 Details
CP3D_867
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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1CP NAME: COPROPORPHYRIN I
FORMULA: C36 H44 N4 O8
SMILES: Cc1c2Cc3[nH]c(Cc4[nH]c(Cc5[nH]c(Cc([nH]2)c1CCC(O)=O)c(C)c5CCC(O)=O)c(C)c4CCC(O)=O)c(C)c3CCC(O)=O
CO2 NAME: CARBON DIOXIDE
FORMULA: C1 O2
SMILES: O=C=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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