university lille north of france LigASite database of binding sites
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LigASite v9.7 (nr25) - non-redundant
LigASite v9.7 (redundant) - redundant
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Browse dataset
holo-structureHelp

PDB ID and HEADER, TITLE and COMPND records of the PDB file.

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3kco
ISOMERASE HEADER
ROOM TEMPERATURE NEUTRON STRUCTURE OF D-XYLOSE ISOMERASE IN WITH TWO NI2+ CATIONS AND D12-D-GLUCOSE IN THE LINEAR FORM JOINTLY WITH X-RAY STRUCTURE 3KBN) TITLE
XYLOSE ISOMERASE 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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GLO S 401
16P TRP
26A PHE
54P HIS
88P MET
90P THR
91P THR
94P PHE
135P VAL
137P TRP
181P GLU
183P LYS
220P HIS
245P ASP
255P ASP
257P ASP
287P ASP
289P LYS
GLO N 401
16K TRP
26F PHE
54K HIS
88K MET
90K THR
91K THR
94K PHE
135K VAL
137K TRP
181K GLU
183K LYS
220K HIS
245K ASP
255K ASP
257K ASP
287K ASP
289K LYS
GLO I 401
16F TRP
26K PHE
54F HIS
88F MET
90F THR
91F THR
94F PHE
135F VAL
137F TRP
181F GLU
183F LYS
220F HIS
245F ASP
255F ASP
257F ASP
287F ASP
289F LYS
GLO D 401
16A TRP
26P PHE
54A HIS
88A MET
90A THR
91A THR
94A PHE
135A VAL
137A TRP
181A GLU
183A LYS
220A HIS
245A ASP
255A ASP
257A ASP
287A ASP
289A LYS
NI T 393
181P GLU
217P GLU
245P ASP
287P ASP
NI O 393
181K GLU
217K GLU
245K ASP
287K ASP
NI J 393
181F GLU
217F GLU
245F ASP
287F ASP
NI E 393
181A GLU
217A GLU
245A ASP
287A ASP
NI M 391
217K GLU
220K HIS
257K ASP
287K ASP
NI L 392
217K GLU
220K HIS
247K ASN
255K ASP
257K ASP
NI Q 392
217P GLU
220P HIS
247P ASN
255P ASP
257P ASP
NI R 391
217P GLU
220P HIS
257P ASP
287P ASP
NI G 392
217F GLU
219F GLY
220F HIS
247F ASN
255F ASP
257F ASP
NI H 391
217F GLU
220F HIS
255F ASP
257F ASP
287F ASP
NI B 392
217A GLU
219A GLY
220A HIS
247A ASN
255A ASP
257A ASP
NI C 391
217A GLU
220A HIS
255A ASP
257A ASP
287A ASP
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:

» PDB
» CSA
» PDBSum
» CATH
» Scop
» Pfam
» UniProt

LigPlot (hosted at the EBI):

no entry
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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» XML File
» XML Schema
» Coordinates (PDB)
» apo binding site (PDB)
» holo binding site (PDB)
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
2gub Details
other holo-structures
pdb ID Ligand Unique ID
3kbn GLOO_401 _NIM_391 _NIN_393 _NIL_392 Details
GLOT_401 _NIQ_392 _NIS_393 _NIR_391
GLOJ_401 _NIG_392 _NIH_391 _NII_393
GLOE_401 _NIB_392 _NIC_391 _NID_393
3kcl GLCH_401 _CDG_392 _CDF_391 Details
GLCP_401 _CDN_391 _CDO_392
GLCL_401 _CDK_392 _CDJ_391
GLCD_401 _CDB_391 _CDC_392
3kbm GLCH_401 _CDG_392 Details
GLCP_401 _CDO_392
GLCD_401 _CDC_392
GLCL_401 _CDK_392
3cwh XULG_401 _MGI_392 _OHJ_501 _MGH_391 Details
XULL_401 _MGN_392 _MGM_391 _OHO_501
XULQ_401 _OHT_501 _MGS_392 _MGR_391
XULB_401 _MGC_391 _MGD_392 _OHE_501
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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GLO NAME: D-GLUCOSE IN LINEAR FORM
FORMULA: C6 H12 O6
SMILES: OCC(O)C(O)C(O)C(O)C=O
NI NAME: NICKEL (II) ION
FORMULA: NI1
SMILES: [Ni++]
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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