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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1xny
LIGASE HEADER
BIOTIN AND PROPIONYL-COA BOUND TO ACYL-COA CARBOXYLASE BETA SUBUNIT FROM S. COELICOLOR (PCCB) TITLE
PROPIONYL-COA CARBOXYLASE COMPLEX B 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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191 H9601
75D PHE
76D GLY
77D LEU
79D ALA
80D ASN
109D PHE
110D GLY
112D ALA
142D GLY
143D GLY
144D ALA
145D ARG
146D ILE
147D GLN
153D LEU
156D TYR
181D ALA
182D GLY
183D GLY
418C GLY
419C GLY
422C ASP
444C VAL
445C MET
453C ILE
454C LEU
456C ARG
457C ARG
191 G9601
75B PHE
76B GLY
77B LEU
79B ALA
80B ASN
106B PHE
109B PHE
110B GLY
112B ALA
142B GLY
143B GLY
144B ALA
145B ARG
146B ILE
147B GLN
153B LEU
156B TYR
160B PHE
181B ALA
182B GLY
183B GLY
418A GLY
419A GLY
422A ASP
444A VAL
445A MET
453A ILE
454A LEU
456A ARG
457A ARG
191 I9601
75F PHE
76F GLY
77F LEU
79F ALA
80F ASN
109F PHE
110F GLY
112F ALA
142F GLY
143F GLY
144F ALA
145F ARG
146F ILE
147F GLN
153F LEU
156F TYR
181F ALA
182F GLY
183F GLY
204F PHE
418E GLY
419E GLY
422E ASP
444E VAL
445E MET
453E ILE
454E LEU
456E ARG
457E ARG
191 G5601
75A PHE
76A GLY
77A LEU
80A ASN
106A PHE
109A PHE
110A GLY
112A ALA
142A GLY
143A GLY
144A ALA
145A ARG
146A ILE
147A GLN
153A LEU
156A TYR
181A ALA
182A GLY
183A GLY
184A ALA
418B GLY
419B GLY
422B ASP
444B VAL
445B MET
453B ILE
454B LEU
456B ARG
457B ARG
191 H5601
75C PHE
76C GLY
77C LEU
80C ASN
106C PHE
109C PHE
110C GLY
112C ALA
142C GLY
143C GLY
144C ALA
145C ARG
146C ILE
147C GLN
153C LEU
156C TYR
181C ALA
182C GLY
183C GLY
418D GLY
419D GLY
422D ASP
444D VAL
445D MET
453D ILE
454D LEU
456D ARG
457D ARG
191 I5601
75E PHE
76E GLY
77E LEU
80E ASN
106E PHE
109E PHE
110E GLY
112E ALA
142E GLY
143E GLY
144E ALA
145E ARG
146E ILE
147E GLN
153E LEU
156E TYR
181E ALA
182E GLY
183E GLY
184E ALA
418F GLY
419F GLY
422F ASP
444F VAL
445F MET
453F ILE
454F LEU
456F ARG
457F ARG
BTN H9600
182D GLY
183D GLY
205D ILE
206D THR
210D VAL
214D VAL
347C CYS
377C PRO
378C GLY
379C PHE
381C PRO
417C PHE
418C GLY
419C GLY
420C ALA
444C VAL
445C MET
BTN G9600
182B GLY
183B GLY
205B ILE
206B THR
210B VAL
214B VAL
347A CYS
377A PRO
378A GLY
379A PHE
381A PRO
417A PHE
418A GLY
419A GLY
420A ALA
444A VAL
445A MET
BTN I9600
182F GLY
183F GLY
205F ILE
206F THR
210F VAL
214F VAL
347E CYS
377E PRO
378E GLY
379E PHE
381E PRO
417E PHE
418E GLY
419E GLY
420E ALA
444E VAL
445E MET
BTN G5600
182A GLY
183A GLY
205A ILE
206A THR
210A VAL
214A VAL
347B CYS
377B PRO
378B GLY
379B PHE
381B PRO
417B PHE
418B GLY
419B GLY
420B ALA
445B MET
BTN H5600
182C GLY
183C GLY
205C ILE
206C THR
210C VAL
214C VAL
347D CYS
377D PRO
378D GLY
379D PHE
381D PRO
417D PHE
418D GLY
419D GLY
420D ALA
445D MET
BTN I5600
182E GLY
183E GLY
205E ILE
206E THR
210E VAL
214E VAL
347F CYS
377F PRO
378F GLY
379F PHE
381F PRO
417F PHE
418F GLY
419F GLY
420F ALA
445F MET
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
1xo6 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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191 NAME: PROPIONYL COENZYME A
FORMULA: C24 H41 N7 O17 P3 S1
SMILES: CCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)[N+]2=[c]3nc[nH]c(N)c3N=C2
BTN NAME: BIOTIN
FORMULA: C10 H16 N2 O3 S1
SMILES: OC(=O)CCCCC1SCC2NC(=O)NC12
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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