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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3hb4
OXIDOREDUCTASE HEADER
17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE1 COMPLEXED WITH E2B TITLE
ESTRADIOL 17-BETA-DEHYDROGENASE 1 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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E2B B 700
92B GLY
93B LEU
94B GLY
95B LEU
96B LEU
142B SER
143B VAL
144B GLY
147B MET
149B LEU
152B ASN
155B TYR
159B LYS
185B CYS
186B GLY
187B PRO
192B PHE
193B MET
196B VAL
218B TYR
221B HIS
222B SER
225B VAL
226B PHE
259B PHE
262B LEU
279B MET
282B GLU
283B VAL
E2B A 700
92A GLY
93A LEU
94A GLY
95A LEU
96A LEU
142A SER
143A VAL
144A GLY
147A MET
149A LEU
152A ASN
155A TYR
159A LYS
185A CYS
186A GLY
187A PRO
192A PHE
193A MET
196A VAL
218A TYR
221A HIS
222A SER
225A VAL
226A PHE
259A PHE
262A LEU
279A MET
282A GLU
283A VAL
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
1bhs Details
other holo-structures
pdb ID Ligand Unique ID
3dhe ANDB_400 Details
ANDD_400
3dey DHTB_732 Details
DHTE_732
1qyw 5SDG_500 Details
5SDC_500
NAPF_361
NAPB_361
3km0 AOMF___1 NAPE_360 Details
AOMC___1 NAPB_360
1qyx ASDD_500 Details
NAPF_361
ASDH_500
NAPB_361
1dht DHTD_400 Details
DHTB_400
3klp B81A_328 Details
B81B_328
1jtv TESB_500 Details
TESE_500
1equ EQIC_329 NAPB_328 Details
NAPE_328
1qyv NAPE_361 Details
NAPB_361
3hb5 NAPD_360 Details
NAPB_360
E2BC_700
E2BA_700
1i5r GOLG_401 HYCF_328 Details
GOLC_401 HYCB_328
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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E2B NAME: not_found
FORMULA: not_found
SMILES: not_found
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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