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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2p4j
HYDROLASE HEADER
CRYSTAL STRUCTURE OF BETA-SECRETASE BOND TO AN INHIBITOR WITH ISOPHTHALAMIDE DERIVATIVES AT P2-P3 TITLE
BETA-SECRETASE 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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23I B 502
11B GLY
12B GLN
13B GLY
14B TYR
30B LEU
32B ASP
34B GLY
35B SER
36B SER
37B ASN
69B VAL
70B PRO
71B TYR
72B THR
73B GLN
108B PHE
110B ILE
115B TRP
118B ILE
126B ILE
128B ARG
198B TYR
226B ILE
228B ASP
229B SER
230B GLY
231B THR
232B THR
233B ASN
235B ARG
307B ARG
325B SER
329B THR
332B VAL
335B ALA
23I C 503
11C GLY
12C GLN
13C GLY
14C TYR
30C LEU
32C ASP
34C GLY
35C SER
37C ASN
69C VAL
70C PRO
71C TYR
72C THR
73C GLN
108C PHE
110C ILE
115C TRP
118C ILE
126C ILE
128C ARG
198C TYR
226C ILE
228C ASP
229C SER
230C GLY
231C THR
232C THR
233C ASN
235C ARG
307C ARG
325C SER
329C THR
332C VAL
335C ALA
23I D 504
11D GLY
12D GLN
13D GLY
14D TYR
30D LEU
32D ASP
34D GLY
35D SER
36D SER
37D ASN
69D VAL
70D PRO
71D TYR
72D THR
73D GLN
108D PHE
110D ILE
115D TRP
118D ILE
126D ILE
128D ARG
198D TYR
224D LYS
226D ILE
228D ASP
229D SER
230D GLY
231D THR
232D THR
233D ASN
235D ARG
307D ARG
325D SER
329D THR
332D VAL
335D ALA
23I A 501
11A GLY
12A GLN
13A GLY
14A TYR
30A LEU
32A ASP
34A GLY
35A SER
37A ASN
69A VAL
70A PRO
71A TYR
72A THR
73A GLN
107A LYS
108A PHE
110A ILE
115A TRP
118A ILE
126A ILE
128A ARG
198A TYR
226A ILE
228A ASP
229A SER
230A GLY
231A THR
232A THR
233A ASN
235A ARG
307A ARG
325A SER
329A THR
332A VAL
335A ALA
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
1sgz Details
other holo-structures
pdb ID Ligand Unique ID
3ufl 508P_449 GOLO_455 Details
508G_449 GOLF_455
1xs7 MMID_386 Details
2g94 ZPQB2001 Details
ZPQA1001
ZPQD4001
ZPQC3001
2vkm BSDD1386 Details
BSDA1386
BSDC1386
BSDB1386
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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23I 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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