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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2e3r
LIPID TRANSPORT HEADER
CRYSTAL STRUCTURE OF CERT START DOMAIN IN COMPLEX WITH C18- CERAMIDE (P1) TITLE
LIPID-TRANSFER PROTEIN CERT 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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18C A1100
436A PHE
442A ARG
445A TRP
446A GLU
447A THR
448A THR
449A ILE
467A GLN
469A HIS
470A LYS
471A ARG
472A VAL
473A TRP
475A ALA
476A SER
478A ARG
480A VAL
482A TYR
504A ASN
521A ALA
523A ILE
525A VAL
553A TYR
557A VAL
559A PRO
563A ALA
564A PRO
567A VAL
568A LEU
571A VAL
572A ALA
574A ARG
575A GLU
576A TYR
578A LYS
579A PHE
18C B1200
436B PHE
442B ARG
445B TRP
446B GLU
447B THR
448B THR
467B GLN
469B HIS
470B LYS
471B ARG
472B VAL
473B TRP
475B ALA
476B SER
478B ARG
480B VAL
482B TYR
504B ASN
521B ALA
523B ILE
525B VAL
553B TYR
557B VAL
559B PRO
563B ALA
564B PRO
567B VAL
568B LEU
571B VAL
572B ALA
574B ARG
575B GLU
576B TYR
579B PHE
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
2e3m Details
other holo-structures
pdb ID Ligand Unique ID
2e3n 6CMA_600 Details
3h3s H15B_600 Details
H15A_600
2e3q 18CA_600 Details
2z9y DDRA___1 Details
3h3t 16HA_600 Details
16HB_600
2e3o 16CA_600 Details
3h3q H13B_600 Details
H13A_600
2e3p 16CB_700 Details
16CA_600
3h3r 14HA_600 Details
14HB_600
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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18C 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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