university lille north of france LigASite database of binding sites
apo-structureHelp

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

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2ou1
LIPID BINDING PROTEIN HEADER
STRUCTURES OF APOLIPOPROTEIN A-II AND A LIPID SURROGATE COMPLEX PROVIDE INSIGHTS INTO APOLIPOPROTEIN-LIPID INTERACTIONS TITLE
APOLIPOPROTEIN A-II COMPND
Illustration of Binding SiteHelp

Figure highlighting the binding site residues. Figures were drawn with Molscript (7) and rendered with Raster3D (8). PISA coordinates (3) are used when available (all entries except NMR).

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Contacting ResiduesHelp

List of binding site residues detected in this protein.

Column 1 gives the position, coloured on a yellow-to-red scale depending on the fraction of corresponding holo-structures where the residue is in contact with a ligand.
Column 2 gives the 3-letter amino acid code, coloured according to physico-chemical type.

Chain ID's of residues are not mentioned in this page because all chains in the apo-structure refer to the same protein.

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2 ALA
3 LYS
4 GLU
5 PRO
6 CYS
7 VAL
8 GLU
9 SER
10 LEU
11 VAL
12 SER
13 GLN
14 TYR
15 PHE
16 GLN
17 THR
18 VAL
19 THR
21 TYR
22 GLY
23 LYS
24 ASP
25 LEU
26 MET
27 GLU
28 LYS
29 VAL
30 LYS
32 PRO
33 GLU
36 ALA
37 GLU
38 ALA
40 SER
41 TYR
42 PHE
43 GLU
44 LYS
45 SER
47 GLU
48 GLN
49 LEU
50 THR
51 PRO
52 LEU
53 ILE
54 LYS
55 LYS
56 ALA
57 GLY
58 THR
59 GLU
60 LEU
61 VAL
62 ASN
63 PHE
64 LEU
65 SER
66 TYR
67 PHE
68 VAL
69 GLU
70 LEU
71 GLY
72 THR
73 GLN
74 PRO
75 ALA
76 THR
77 GLN
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:

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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holo-structuresHelp

Table describing the holo-structures and ligands used to define the binding sites.

Column 1 gives the PDB ID of the holo-structure.
Column 2 gives the unique ID of the ligand; a space-separated list of HET-groups that constitute the ligand (see Methods). Each HET-group in the ligand is uniquely identified by a string in which the first four characters are the three-letter HET ID from the PDB file followed by the chain ID from the PISA file, and the last four characters are the residue sequence number from the PDB file.
Column 3 gives the number of atoms in each ligand.
Column 4 gives the number of protein-ligand inter-atomic contacts.

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pdb ID Ligand Unique ID #atoms #contacts
1l6l BOGM1621 20 73 Details
BOGM1620 20 83
BOGA1603 20 97
BOG41714 20 85
BOG31716 20 77
BOG11705 BOGS1704 40 166
BOGY1733 20 88
BOGW1718 20 91
BOG51724 BOGW1723 BOGX1725 60 247
BOGZ1731 20 96
BOGB1602 20 99
BOGF1619 20 114
BOGI1601 10 77
BOGN1618 20 94
BOGH1626 BOGQ1627 40 193
BOGG1634 20 89
BOG21708 20 91
BOGU1710 20 98
BOG51720 20 75
BOGJ1607 20 81
BOG51719 20 93
BOG61717 20 74
BOGB1609 20 98
BOG71726 BOG81727 40 185
BOG11709 20 96
BOGH1629 BOGQ1628 40 174
BOGB1606 20 105
BOGH1631 BOGQ1630 40 224
BOG11707 20 85
BOGN1617 20 86
BOG21703 20 96
BOGU1715 20 108
BOGL1615 20 105
BOGC1614 20 93
BOGD1612 20 104
BOGY1730 20 114
BOG81728 BOGZ1729 40 175
BOGJ1608 20 86
BOGA1604 BOGI1605 40 160
BOGT1706 20 106
BOG31712 20 92
BOGE1623 BOGN1624 40 144
BOGK1610 20 89
BOGM1625 20 92
BOGZ1732 20 94
BOGY1734 20 91
BOGK1616 20 72
BOGT1702 20 100
BOGG1633 BOGP1632 40 177
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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