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 W1718
2K ALA
8W GLU
106 LEU
11W VAL
146 TYR
15W PHE
17W THR
186 VAL
196 THR
21W TYR
BOG M1625
3H LYS
67E PHE
70F LEU
71E GLY
72M THR
73E GLN
74M PRO
75M ALA
76M THR
BOG A1603
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 61717
4W GLU
5W PRO
6W CYS
76 VAL
85 GLU
106 LEU
115 VAL
126 SER
76V THR
77V GLN
BOG 71726
4Z GLU
7Z VAL
87 GLU
10Z LEU
11Y VAL
12Y SER
137 GLN
14Z TYR
15Y PHE
76X THR
77X GLN
BOG 21703
42 GLU
52 PRO
61 CYS
71 VAL
8S GLU
10T LEU
11S VAL
12S SER
14S TYR
15X PHE
215 TYR
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
14B TYR
15A PHE
16I GLN
BOG Q1627
7Q VAL
8P GLU
10Q LEU
11P VAL
12P SER
14H TYR
15P PHE
18G VAL
BOG U1710
7V VAL
8U GLU
104 LEU
11U VAL
123 SER
134 GLN
14V TYR
153 PHE
163 GLN
174 THR
193 THR
BOG 81727
78 VAL
87 GLU
108 LEU
117 VAL
127 SER
14Z TYR
157 PHE
18Y VAL
BOG K1610
7D VAL
8C GLU
10L LEU
11C VAL
12K SER
13L GLN
14L TYR
15K PHE
16K GLN
17L THR
19K THR
BOG F1619
8J GLU
14F TYR
15E PHE
18N VAL
19E THR
21N TYR
22N GLY
23E LYS
25N LEU
26E MET
BOG N1618
8E GLU
10N LEU
11N VAL
13N GLN
14N TYR
15M PHE
16N GLN
17E THR
18N VAL
19N THR
BOG M1620
9J SER
23M LYS
24N ASP
25M LEU
26M MET
27M GLU
28M LYS
29M VAL
30M LYS
BOG B1602
12I SER
14J TYR
15A PHE
17B THR
18B VAL
19A THR
21B TYR
22B GLY
23B LYS
26B MET
BOG T1702
121 SER
142 TYR
15S PHE
17T THR
18T VAL
19S THR
21T TYR
22T GLY
23T LYS
26T MET
BOG 51719
14X TYR
17X THR
18W VAL
19W THR
216 TYR
22W GLY
23W LYS
256 LEU
26W MET
295 VAL
BOG Q1628
14Q TYR
15G PHE
17H THR
18G VAL
19G THR
21H TYR
BOG 81728
148 TYR
15Y PHE
17Z THR
18Y VAL
19Y THR
21Z TYR
BOG Z1731
154 PHE
45Z SER
48Z GLN
49Y LEU
517 PRO
52Y LEU
53Z ILE
557 LYS
BOG H1631
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 Z1729
178 THR
188 VAL
197 THR
218 TYR
227 GLY
25Z LEU
26Y MET
29Z VAL
BOG 11705
181 VAL
191 THR
212 TYR
221 GLY
241 ASP
25T LEU
261 MET
28T LYS
29T VAL
32T PRO
33T GLU
BOG D1612
18D VAL
21K TYR
22D GLY
25L LEU
26K MET
28L LYS
29C VAL
32L PRO
33C GLU
BOG 31712
18V VAL
213 TYR
22V GLY
254 LEU
263 MET
284 LYS
294 VAL
324 PRO
33U GLU
BOG I1605
19I THR
21J TYR
22I GLY
24I ASP
25B LEU
28B LYS
29B VAL
32B PRO
33B GLU
BOG S1704
212 TYR
25T LEU
26S MET
28T LYS
29S VAL
30S LYS
32S PRO
33S GLU
36S ALA
37S GLU
BOG A1604
21J TYR
25B LEU
26A MET
28B LYS
29A VAL
30A LYS
32A PRO
33A GLU
36A ALA
37A GLU
BOG 51720
235 LYS
246 ASP
255 LEU
265 MET
275 GLU
285 LYS
295 VAL
305 LYS
BOG Z1732
304 LYS
598 GLU
607 LEU
627 ASN
638 PHE
64Z LEU
657 SER
667 TYR
677 PHE
697 GLU
BOG B1606
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
41Q TYR
42G PHE
44H LYS
45G SER
48G GLN
BOG Y1730
37Z GLU
388 ALA
40Z SER
41Z TYR
42Y PHE
44Z LYS
458 SER
488 GLN
BOG T1706
372 GLU
381 ALA
401 SER
411 TYR
421 PHE
431 GLU
441 LYS
45T SER
481 GLN
BOG 41714
41V TYR
44U LYS
45U SER
47U GLU
48V GLN
494 LEU
504 THR
524 LEU
534 ILE
544 LYS
BOG C1614
41L TYR
44D LYS
45L SER
47C GLU
48C GLN
49C LEU
50L THR
52L LEU
53L ILE
54L LYS
BOG J1607
47A GLU
48I GLN
49I LEU
51A PRO
52A LEU
53J ILE
55A LYS
BOG 11707
47S GLU
48T GLN
49T LEU
51S PRO
52S LEU
532 ILE
55S LYS
BOG M1621
51N PRO
52M LEU
53M ILE
54N LYS
55N LYS
56M ALA
57M GLY
58N THR
61M VAL
BOG 21708
562 ALA
59S GLU
60S LEU
62S ASN
63T PHE
642 LEU
66S TYR
67S PHE
BOG W1723
58W THR
606 LEU
62W ASN
63W PHE
646 LEU
65W SER
666 TYR
675 PHE
BOG U1715
58U THR
593 GLU
60U LEU
62U ASN
63V PHE
644 LEU
65U SER
66U TYR
674 PHE
BOG L1615
58C THR
59K GLU
60C LEU
62C ASN
63K PHE
64L LEU
66C TYR
67L PHE
BOG J1608
58A THR
59A GLU
60A LEU
62A ASN
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 Y1733
608 LEU
62Y ASN
63Z PHE
648 LEU
65Y SER
66Y TYR
67Z PHE
688 VAL
69Y GLU
BOG B1609
60B LEU
62I ASN
63J PHE
64B LEU
65I SER
66J TYR
67A PHE
69I GLU
70A LEU
BOG 11709
60T LEU
621 ASN
632 PHE
64T LEU
651 SER
662 TYR
672 PHE
691 GLU
BOG E1623
60N LEU
62E ASN
63N PHE
64N LEU
65N SER
66E TYR
67N PHE
68N VAL
BOG N1624
62E ASN
63E PHE
66E TYR
67N PHE
68M VAL
70E LEU
71M GLY
BOG 31716
633 PHE
64V LEU
66U TYR
673 PHE
693 GLU
703 LEU
BOG 51724
63W PHE
66W TYR
67W PHE
685 VAL
69W GLU
706 LEU
715 GLY
73W GLN
BOG Y1734
63Z PHE
66Z TYR
67Y PHE
688 VAL
69Y GLU
70Z LEU
718 GLY
728 THR
73Y GLN
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 X1725
66X TYR
67W PHE
695 GLU
70X LEU
715 GLY
735 GLN
74X PRO
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
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
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
Script execution time: 2.8113 seconds