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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1l6l
LIPID TRANSPORT HEADER
STRUCTURES OF APOLIPOPROTEIN A-II AND A LIPID SURROGATE COMPLEX PROVIDE INSIGHTS INTO APOLIPOPROTEIN-LIPID INTERACTIONS TITLE
MOL_ID: 1; MOLECULE: APOLIPOPROTEIN A-II; CHAIN: A, B, C, D, E, F, G, H, I, J, K, L, M, N, P, Q, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4, 5, 6, 7, 8; SYNONYM: APO-AII, APOA-II 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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BOG F1625
3H LYS
67E PHE
70F LEU
71E GLY
72M THR
73E GLN
74M PRO
75M ALA
76M THR
BOG J1603
4J GLU
6J CYS
7I VAL
8I GLU
10B LEU
11A VAL
12A SER
14A TYR
15F PHE
BOG H1626
4H GLU
7P VAL
8P GLU
10H LEU
11P VAL
12G SER
14G TYR
15G PHE
76F THR
BOG N1617
5F PRO
6F CYS
7N VAL
8M GLU
10N LEU
11N VAL
12N SER
15N PHE
73D GLN
75C ALA
76C THR
BOG I1601
6I CYS
7I VAL
8I GLU
9I SER
10J LEU
11J VAL
12I SER
13J GLN
14J TYR
15A PHE
16I GLN
BOG G1627
7Q VAL
11Q VAL
14Q TYR
18G VAL
BOG Q1627
7Q VAL
8P GLU
10Q LEU
11Q VAL
12P SER
14Q TYR
15P PHE
BOG C1610
7D VAL
8C GLU
10L LEU
11C VAL
12K SER
13L GLN
14L TYR
15K PHE
16K GLN
17L THR
19K THR
BOG E1618
8E GLU
10N LEU
11N VAL
14N TYR
15M PHE
BOG N1618
8E GLU
10N LEU
11N VAL
13N GLN
14N TYR
15E PHE
16N GLN
17E THR
18N VAL
19N THR
BOG B1601
8I GLU
12I SER
14B TYR
15A PHE
BOG F1619
8J GLU
14F TYR
15E PHE
18N VAL
19E THR
21N TYR
22N GLY
23E LYS
25N LEU
26E MET
BOG H1627
8P GLU
10Q LEU
11P VAL
12P SER
15G PHE
BOG M1620
9J SER
23M LYS
24N ASP
25M LEU
26M MET
27M GLU
28M LYS
29M VAL
30M LYS
BOG P1627
11P VAL
12P SER
14H TYR
15P PHE
BOG B1602
12I SER
14J TYR
15A PHE
17B THR
18B VAL
19A THR
21B TYR
22B GLY
23B LYS
26B MET
BOG G1628
14Q TYR
15G PHE
17H THR
18G VAL
19G THR
21H TYR
BOG P1631
15L PHE
47P GLU
48H GLN
49G LEU
51P PRO
52G LEU
53H ILE
54P LYS
55P LYS
58P THR
BOG H1629
17Q THR
18Q VAL
19P THR
21Q TYR
22P GLY
25H LEU
26G MET
29H VAL
BOG D1612
18D VAL
21K TYR
22D GLY
25L LEU
26K MET
28L LYS
29C VAL
32L PRO
33C GLU
BOG I1605
19I THR
21J TYR
22I GLY
24I ASP
25B LEU
28B LYS
29B VAL
32B PRO
33B GLU
BOG A1604
21J TYR
25B LEU
26A MET
28B LYS
29A VAL
30A LYS
32A PRO
33A GLU
36A ALA
37A GLU
BOG B1605
25I LEU
29B VAL
32B PRO
33B GLU
BOG I1606
37J GLU
38J ALA
40I SER
41I TYR
42I PHE
43I GLU
44I LYS
45B SER
48I GLN
BOG Q1630
37H GLU
38Q ALA
40H SER
41H TYR
42P PHE
BOG H1630
40H SER
41Q TYR
42G PHE
44H LYS
45G SER
48G GLN
BOG C1614
41L TYR
44D LYS
45L SER
48C GLN
49C LEU
BOG B1606
41B TYR
42B PHE
44I LYS
45B SER
BOG L1614
44C LYS
47C GLU
48C GLN
49L LEU
50L THR
52L LEU
53L ILE
54L LYS
BOG J1607
47A GLU
48B GLN
49A LEU
51A PRO
52I LEU
53J ILE
55A LYS
BOG B1607
48I GLN
49I LEU
52A LEU
BOG M1621
51N PRO
52M LEU
53M ILE
54N LYS
55N LYS
56M ALA
57M GLY
58N THR
61M VAL
BOG L1615
58C THR
59K GLU
60C LEU
62C ASN
63K PHE
64L LEU
66C TYR
67L PHE
BOG A1608
58A THR
60J LEU
62A ASN
63A PHE
66A TYR
BOG B1608
59A GLU
60A LEU
63A PHE
64J LEU
66A TYR
67A PHE
BOG G1633
59Q GLU
60Q LEU
62Q ASN
63H PHE
64Q LEU
65G SER
66G TYR
67H PHE
69G GLU
BOG P1632
59G GLU
60G LEU
62P ASN
63G PHE
64H LEU
65P SER
66P TYR
67P PHE
69P GLU
BOG N1623
60N LEU
62E ASN
63N PHE
64N LEU
65N SER
66E TYR
67N PHE
68N VAL
BOG I1609
60B LEU
62I ASN
63J PHE
64B LEU
65I SER
66J TYR
67I PHE
69I GLU
BOG M1624
62E ASN
63E PHE
66E TYR
67N PHE
68M VAL
70E LEU
71M GLY
BOG B1609
63J PHE
66J TYR
67A PHE
70A LEU
BOG K1616
63K PHE
64D LEU
66K TYR
67C PHE
70D LEU
71K GLY
BOG G1634
64Q LEU
66H TYR
67Q PHE
68Q VAL
69G GLU
70P LEU
71Q GLY
72Q THR
73G GLN
BOG E1625
67E PHE
70F LEU
71E GLY
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):

» Jmol
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
2ou1 Details
other holo-structures
pdb ID Ligand Unique ID
none
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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BOG NAME: B-OCTYLGLUCOSIDE
FORMULA: C14 H28 O6
SMILES: CCCCCCCCOC1OC(CO)C(O)C(O)C1O
v6.0
October 2008
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
Script execution time: 1.0627 seconds