EBI Databases Structure Databases PDBsum

Ligand clusters for UniProt code P02945

Ligand clusters for P02945: Bacteriorhodopsin OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=bop PE=1 SV=2

4 ligand clusters


Cluster 1. 38 ligand types 964 ligands		Cluster 2. 3 ligand types 147 ligands		Cluster 3. 1 ligand type 1 ligand		Cluster 4. 1 ligand type 1 ligand

Representative protein: 1r2nA

Structures

PDB		Schematic diagram

1r2nA
6rqoA
1p8uA
6g7lA
6g7jA
		more ...

Cluster 1 contains 38 ligand types (of which only 20 are listed. Click for all)

Use checkboxes to select ligands to display in RasMol, Jmol, or download as an SDF file.
Selection shortcuts: select all/none invert selection.

Ligand

Description

1. Ligand: MC3 × 2

dl-dimyristoylphosphatidylcholine

1,2-Dimyristoyl-Rac-Glycero-3-Phosphocholine

PDB codes: 3utv(A), 3utw(A).

2. Ligand: SQL × 2

squalene

(6e,10e,14e,18e)-2,6,10,15,19,23-Hexamethyltetracosa-2, 6,10,14,18,22-Hexaene

PDB codes: 4md1(A), 4md2(A).

3. Ligand: LI1 × 296

1-[2,6,10.14-Tetramethyl-Hexadecan-16-Yl]-2-[2,10,14- Trimethylhexadecan-16-Yl]glycerol

PDB codes: 1c3w(A), 1c8r(A), 1c8s(A), 1f4z(A), 1f50(A), 1jv6(A), 1jv7(A), 1kg8(A), 1kg9(A), 1kgb(A), 1m0k(A), 1m0l(A), 1m0m(A), 1mgy(A), 1o0a(A), 1p8h(A), 1p8i(A), 1p8u(A), 1s8j(A), 1s8l(A), 2i1x(A), 2i20(A), 2i21(A), 2wjk(A), 3ns0(A), 3nsb(A), 3t45(A), 4fpd(A), 4x31(A), 4x32(A), 5a44(A), 5j7a(A), 6g7h(A), 6g7i(A), 6g7j(A), 6g7k(A), 6g7l(A), 6rqp(A),

4. Ligand: L2P × 148

2,3-Di-Phytanyl-Glycerol

PDB codes: 1dze(A), 1iw6(A), 1iw9(A), 1ixf(A), 1qm8(A), 1ucq(A), 1x0i(1), 1x0k(1), 1x0s(A), 2zfe(A), 2zzl(A), 4md1(A), 4md2(A), 5b6v(A), 5b6w(A), 5b6x(A), 5b6y(A), 5b6z(A), 5h2h(A), 5h2i(A), 5h2j(A), 5h2k(A), 5h2l(A), 5h2m(A), 5h2n(A), 5h2o(A), 5h2p(A), 5zil(A), 5zim(A), 5zin(A), 6ga1(A), 6ga2(A), 6ga3(A), 6ga4(A), 6ga5(A), 6ga6(A), 6ga7(A), 6ga8(A), 6ga9(A), 6gaa(A), 6gab(A), 6gac(A), 6gad(A), 6gae(A), 6gaf(A), 6gag(A), 6gah(A), 6gai(A),

5. Ligand: OCT × 85

N-Octane

PDB codes: 1xji(A), 4hyx(A), 5b34(A), 5b6v(A), 5b6w(A), 5b6x(A), 5b6y(A), 5b6z(A), 5h2h(A), 5h2i(A), 5h2j(A), 5h2k(A), 5h2l(A), 5h2m(A), 5h2n(A), 5h2o(A), 5h2p(A), 6ga1(A), 6ga2(A), 6ga3(A), 6ga4(A), 6ga5(A), 6ga6(A), 6ga7(A), 6ga8(A), 6ga9(A), 6gaa(A), 6gab(A), 6gac(A), 6gad(A), 6gae(A), 6gaf(A), 6gag(A), 6gah(A), 6gai(A),

6. Ligand: UND × 64

Undecane

PDB codes: 5b6v(A), 5b6w(A), 5b6x(A), 5b6y(A), 5b6z(A), 5h2h(A), 5h2i(A), 5h2j(A), 5h2k(A), 5h2l(A), 5h2m(A), 5h2n(A), 5h2o(A), 5h2p(A), 6ga1(A), 6ga2(A), 6ga3(A), 6ga4(A), 6ga5(A), 6ga6(A), 6ga7(A), 6ga8(A), 6ga9(A), 6gaa(A), 6gab(A), 6gac(A), 6gad(A), 6gae(A), 6gaf(A), 6gag(A), 6gah(A), 6gai(A),

7. Ligand: D10 × 50

Decane

PDB codes: 1xji(A), 3hap(A), 3has(A), 4hyx(A), 5b34(A), 5b6v(A), 5b6w(A), 5b6x(A), 5b6y(A), 5b6z(A), 5h2h(A), 5h2i(A), 5h2j(A), 5h2k(A), 5h2l(A), 5h2m(A), 5h2n(A), 5h2o(A), 5h2p(A), 6ga1(A), 6ga2(A), 6ga3(A), 6ga4(A), 6ga5(A), 6ga6(A), 6ga7(A), 6ga8(A), 6ga9(A), 6gaa(A), 6gab(A), 6gac(A), 6gad(A), 6gae(A), 6gaf(A), 6gag(A), 6gah(A), 6gai(A).

8. Ligand: MYS × 46

Pentadecane

9. Ligand: DD9 × 37

Nonane

PDB codes: 3hap(A), 3haq(A), 5b34(A), 5b6v(A), 5b6w(A), 5b6x(A), 5b6y(A), 5b6z(A), 5h2h(A), 5h2i(A), 5h2j(A), 5h2k(A), 5h2l(A), 5h2m(A), 5h2n(A), 5h2o(A), 5h2p(A), 6ga1(A), 6ga2(A), 6ga3(A), 6ga4(A), 6ga5(A), 6ga6(A), 6ga7(A), 6ga8(A), 6ga9(A), 6gaa(A), 6gab(A), 6gac(A), 6gad(A), 6gae(A), 6gaf(A), 6gag(A), 6gah(A), 6gai(A).

10. Ligand: C14 × 33

Tetradecane

PDB codes: 1xji(A), 5b6v(A), 5b6w(A), 5b6x(A), 5b6y(A), 5b6z(A), 5h2h(A), 5h2i(A), 5h2j(A), 5h2k(A), 5h2l(A), 5h2m(A), 5h2n(A), 5h2o(A), 5h2p(A), 6ga1(A), 6ga2(A), 6ga3(A), 6ga4(A), 6ga5(A), 6ga6(A), 6ga7(A), 6ga8(A), 6ga9(A), 6gaa(A), 6gab(A), 6gac(A), 6gad(A), 6gae(A), 6gaf(A), 6gag(A), 6gah(A), 6gai(A).

11. Ligand: TRD × 32

Tridecane

12. Ligand: L3P × 25

2,3-Di-O-Phytanly-3-Sn-Glycero-1-Phosphoryl-3'-Sn- Glycerol-1'-Phosphate

PDB codes: 1dze(A), 1iw6(A), 1iw9(A), 1ixf(A), 1qm8(A), 1ucq(A), 1x0i(1), 1x0k(1), 1x0s(A), 2zfe(A), 2zzl(A).

13. Ligand: OLC × 21

(2r)-2,3-Dihydroxypropyl (9z)-Octadec-9-Enoate

PDB codes: 6g7h(A), 6g7i(A), 6g7j(A), 6g7k(A), 6g7l(A), 6rqp(A),

14. Ligand: SQU × 17

2,10,23-Trimethyl-Tetracosane

PDB codes: 1c3w(A), 1c8r(A), 1c8s(A), 1f4z(A), 1f50(A), 1kme(A), 1m0k(A), 1m0l(A), 1m0m(A), 1o0a(A), 1p8h(A), 1p8i(A), 1p8u(A), 2i1x(A), 2i20(A), 2i21(A).

15. Ligand: D12 × 13

Dodecane

PDB codes: 1xji(A), 3hap(A), 3haq(A), 3has(A), 3uty(A), 5b34(A),

16. Ligand: LFA × 12

Eicosane

PDB codes: 4xxj(A),

17. Ligand: DPG × 10

Phosphoric acid 2,3-Bis-(3,7,11,15-Tetramethyl- Hexadecyloxy)-Propyl ester 2-Hydroxo-3-
Phosphonooxy- Propyl ester

PDB codes: 1bm1(A), 2brd(A),

18. Ligand: GLC-MAN-GAL × 8

GLC=Alpha-D-Glucose, MAN=Alpha-D-Mannose, GAL=Beta-D-Galactose.

PDB codes: 1dze(A), 1iw6(A), 1iw9(A), 1ixf(A), 1qm8(A), 1ucq(A), 1x0k(1), 1x0s(A).

19. Ligand: PH1 × 8

1,2-[Di-2,6,10,14-Tetramethyl-Hexadecan-16-Oxy]-Propane

PDB codes: 1qhj(A),

20. Ligand: 2DP × 7

3-[[3-Methylphosphono-Glycerolyl]phosphonyl]-[1,2-Di[2, 6,10,14-Tetramethyl-Hexadecan-16-
Yl]glycerol

PDB codes: 2at9(A),

+ more. Press

for full list

Cluster 2 contains 3 ligand types

Selection shortcuts: select all/none invert selection.

Ligand

Description

1. Ligand: RET × 145

Retinal

PDB codes: 1ap9(A), 1at9(A), 1bm1(A), 1brd(A), 1brr(A), 1brx(A), 1c3w(A), 1c8r(A), 1c8s(A), 1dze(A), 1e0p(A), 1f4z(A), 1f50(A), 1fbb(A), 1fbk(A), 1iw6(A), 1iw9(A), 1ixf(A), 1jv6(A), 1jv7(A), 1kg8(A), 1kg9(A), 1kgb(A), 1kme(A), 1m0k(A), 1m0l(A), 1m0m(A), 1mgy(A), 1o0a(A), 1p8h(A), 1p8i(A), 1p8u(A), 1pxr(A), 1pxs(A), 1py6(A), 1q5i(A), 1q5j(A), 1qhj(A), 1qko(A), 1qkp(A), 1qm8(A), 1r2n(A), 1r84(A), 1s51(A), 1s52(A), 1s53(A), 1s54(A), 1s8j(A), 1s8l(A), 1tn0(A), 1tn5(A), 1ucq(A), 1vjm(A), 1x0i(1), 1x0k(1), 1x0s(A), 1xji(A), 2at9(A), 2brd(A), 2i1x(A), 2i20(A), 2i21(A), 2ntu(A), 2ntw(A), 2wjk(A), 2wjl(A), 2zfe(A), 2zzl(A), 3coc(A), 3cod(A), 3han(A), 3hao(A), 3hap(A), 3haq(A), 3har(A), 3has(A), 3mbv(A), 3ns0(A), 3nsb(A), 3t45(A), 3utv(A), 3utw(A), 3utx(A), 3uty(A), 3vhz(A), 3vi0(A), 4fpd(A), 4hwl(A), 4hyx(A), 4md1(A), 4md2(A), 4ov0(A), 4x31(A), 4x32(A), 5a44(A), 5a45(A), 5b34(A), 5b6v(A), 5b6w(A), 5b6x(A), 5b6y(A), 5b6z(A), 5br2(A), 5br5(A), 5h2h(A), 5h2i(A), 5h2j(A), 5h2k(A), 5h2l(A), 5h2m(A), 5h2n(A), 5h2o(A), 5h2p(A), 5j7a(A), 5zil(A), 5zim(A), 5zin(A), 6g7h(A), 6g7i(A), 6g7j(A), 6g7k(A), 6g7l(A), 6ga1(A), 6ga2(A), 6ga3(A), 6ga4(A), 6ga5(A), 6ga6(A), 6ga7(A), 6ga8(A), 6ga9(A), 6gaa(A), 6gab(A), 6gac(A), 6gad(A), 6gae(A), 6gaf(A), 6gag(A), 6gah(A), 6gai(A), 6rmk(A), 6rnj(A), 6rph(A), 6rqo(A), 6rqp(A).

2. Ligand: NO3 × 1

Nitrate ion

PDB code: 1s8j(A).

_Br

3. Metal: _BR × 1

PDB code: 1mgy(A).

Ligand clusters for UniProt code P02945

Ligand clusters for P02945: Bacteriorhodopsin OS=Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) OX=64091 GN=bop PE=1 SV=2

Structures

Cluster 1 contains 38 ligand types (of which only 20 are listed. Click for all)

Cluster 2 contains 3 ligand types

Cluster 3 contains 1 ligand type

Cluster 4 contains 1 ligand type