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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4tpi
HYDROLASE/HYDROLASE INHIBITOR HEADER
THE REFINED 2.2-ANGSTROMS (0.22-NM) X-RAY CRYSTAL STRUCTURE OF THE TERNARY COMPLEX FORMED BY BOVINE TRYPSINOGEN, VALINE-VALINE AND THE ARG15 ANALOGUE OF BOVINE PANCREATIC TRYPSIN INHIBITOR TITLE
TRYPSINOGEN 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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VAL P1017
17P VAL
18P GLY
19P GLY
143P ASN
144P THR
145P LYS
146P SER
158P LEU
188P GLY
189P ASP
191P CYS
220P CYS
221P ALA
VAL F1017
17F VAL
18F GLY
19F GLY
143F ASN
144F THR
145F LYS
146F SER
158F LEU
188F GLY
189F ASP
191F CYS
220F CYS
221F ALA
VAL K1017
17K VAL
18K GLY
19K GLY
143K ASN
144K THR
145K LYS
146K SER
158K LEU
188K GLY
189K ASP
191K CYS
220K CYS
221K ALA
VAL A1017
17A VAL
18A GLY
19A GLY
143A ASN
144A THR
145A LYS
146A SER
158A LEU
188A GLY
189A ASP
191A CYS
220A CYS
221A ALA
VAL P1016
19P GLY
138P ILE
139P SER
140P GLY
142P GLY
143P ASN
144P THR
156P LYS
157P CYS
158P LEU
189P ASP
190P SER
194P ASP
VAL F1016
19F GLY
138F ILE
139F SER
140F GLY
142F GLY
143F ASN
144F THR
156F LYS
157F CYS
158F LEU
189F ASP
190F SER
194F ASP
VAL A1016
19A GLY
138A ILE
139A SER
140A GLY
142A GLY
143A ASN
144A THR
156A LYS
157A CYS
158A LEU
189A ASP
190A SER
194A ASP
VAL K1016
19K GLY
138K ILE
139K SER
140K GLY
142K GLY
143K ASN
144K THR
156K LYS
157K CYS
158K LEU
189K ASP
190K SER
194K 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:

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
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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
1tgn Details
other holo-structures
pdb ID Ligand Unique ID
2tpi ILEA1016 VALA1017 Details
3tpi ILEP1016 VALP1017 Details
ILEF1016 VALF1017
ILEK1016 VALK1017
ILEA1016 VALA1017
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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VAL NAME: L-Valine
FORMULA: C5 H10 N1 O2
SMILES: CC(C)C(N)C(O)=OVALINE
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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