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
75J PHE
76J GLY
77J LEU
79J ALA
80J ASN
109J PHE
110J GLY
112J ALA
142J GLY
143J GLY
144J ALA
145J ARG
146J ILE
147J GLN
153J LEU
156J TYR
181J ALA
182J GLY
183J GLY
204J PHE
418G GLY
419G GLY
422G ASP
444G VAL
445G MET
453G ILE
454G LEU
456G ARG
457G ARG
191 N9601
75P PHE
76P GLY
77P LEU
79P ALA
80P ASN
109P PHE
110P GLY
112P ALA
142P GLY
143P GLY
144P ALA
145P ARG
146P ILE
147P GLN
153P LEU
156P TYR
181P ALA
182P GLY
183P GLY
418M GLY
419M GLY
422M ASP
444M VAL
445M MET
453M ILE
454M LEU
456M ARG
457M ARG
191 Q5601
75M PHE
76M GLY
77M LEU
80M ASN
106M PHE
109M PHE
110M GLY
112M ALA
142M GLY
143M GLY
144M ALA
145M ARG
146M ILE
147M GLN
153M LEU
156M TYR
181M ALA
182M GLY
183M GLY
418P GLY
419P GLY
422P ASP
444P VAL
445P MET
453P ILE
454P LEU
456P ARG
457P ARG
191 E5601
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
418D GLY
419D GLY
422D ASP
444D VAL
445D MET
453D ILE
454D LEU
456D ARG
457D ARG
191 B9601
75D PHE
76D GLY
77D LEU
79D ALA
80D ASN
106D PHE
109D PHE
110D GLY
112D ALA
142D GLY
143D GLY
144D ALA
145D ARG
146D ILE
147D GLN
153D LEU
156D TYR
160D PHE
181D ALA
182D GLY
183D GLY
418A GLY
419A GLY
422A ASP
444A VAL
445A MET
453A ILE
454A LEU
456A ARG
457A ARG
191 K5601
75G PHE
76G GLY
77G LEU
80G ASN
106G PHE
109G PHE
110G GLY
112G ALA
142G GLY
143G GLY
144G ALA
145G ARG
146G ILE
147G GLN
153G LEU
156G TYR
181G ALA
182G GLY
183G GLY
184G ALA
418J GLY
419J GLY
422J ASP
444J VAL
445J MET
453J ILE
454J LEU
456J ARG
457J ARG
BTN I9600
182J GLY
183J GLY
205J ILE
206J THR
210J VAL
214J VAL
347G CYS
377G PRO
378G GLY
379G PHE
381G PRO
417G PHE
418G GLY
419G GLY
420G ALA
444G VAL
445G MET
BTN O9600
182P GLY
183P GLY
205P ILE
206P THR
210P VAL
214P VAL
347M CYS
377M PRO
378M GLY
379M PHE
381M PRO
417M PHE
418M GLY
419M GLY
420M ALA
444M VAL
445M MET
BTN R5600
182M GLY
183M GLY
205M ILE
206M THR
210M VAL
214M VAL
347P CYS
377P PRO
378P GLY
379P PHE
381P PRO
417P PHE
418P GLY
419P GLY
420P ALA
445P MET
BTN F5600
182A GLY
183A GLY
205A ILE
206A THR
210A VAL
214A VAL
347D CYS
377D PRO
378D GLY
379D PHE
381D PRO
417D PHE
418D GLY
419D GLY
420D ALA
445D MET
BTN C9600
182D GLY
183D GLY
205D ILE
206D THR
210D VAL
214D VAL
347A CYS
377A PRO
378A GLY
379A PHE
381A PRO
417A PHE
418A GLY
419A GLY
420A ALA
444A VAL
445A MET
BTN L5600
182G GLY
183G GLY
205G ILE
206G THR
210G VAL
214G VAL
347J CYS
377J PRO
378J GLY
379J PHE
381J PRO
417J PHE
418J GLY
419J GLY
420J ALA
445J 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):

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
1xnv 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
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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