- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x RET: RETINAL(Covalent)
- 9 x L2P: 2,3-DI-PHYTANYL-GLYCEROL(Non-covalent)
L2P.2: 23 residues within 4Å:- Chain A: T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147
- Chain B: G.21, T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, A.51, F.54, T.55
- Ligands: UND.16, D10.20, HP6.21
7 PLIP interactions:3 interactions with chain A, 4 interactions with chain B- Hydrophobic interactions: A:A.110, A:Y.147, A:Y.147, B:L.25, B:L.28, B:T.47, B:L.48
L2P.10: 10 residues within 4Å:- Chain A: Y.131, F.135, W.138, A.139, T.142, A.143, L.146, L.190, A.196
- Ligands: UND.9
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:F.135
L2P.11: 28 residues within 4Å:- Chain A: L.48, I.52, T.55, M.56, Y.64, T.67, W.80, Y.83, A.84, L.87, F.88, L.92, L.123, L.127
- Chain C: L.87, V.112, G.113, G.116, I.117, G.120, T.121, L.123, V.124, L.127
- Ligands: C14.14, L2P.27, L2P.43, C14.46
12 PLIP interactions:4 interactions with chain C, 8 interactions with chain A- Hydrophobic interactions: C:L.87, C:I.117, C:L.123, C:V.124, A:I.52, A:I.52, A:W.80, A:W.80, A:W.80, A:F.88, A:L.123
- Hydrogen bonds: A:Y.64
L2P.18: 23 residues within 4Å:- Chain B: T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147
- Chain C: G.21, T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, A.51, F.54, T.55
- Ligands: UND.32, D10.36, HP6.37
7 PLIP interactions:4 interactions with chain C, 3 interactions with chain B- Hydrophobic interactions: C:L.25, C:L.28, C:T.47, C:L.48, B:A.110, B:Y.147, B:Y.147
L2P.26: 10 residues within 4Å:- Chain B: Y.131, F.135, W.138, A.139, T.142, A.143, L.146, L.190, A.196
- Ligands: UND.25
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:F.135
L2P.27: 28 residues within 4Å:- Chain A: L.87, V.112, G.113, G.116, I.117, G.120, T.121, L.123, V.124, L.127
- Chain B: L.48, I.52, T.55, M.56, Y.64, T.67, W.80, Y.83, A.84, L.87, F.88, L.92, L.123, L.127
- Ligands: L2P.11, C14.14, C14.30, L2P.43
12 PLIP interactions:8 interactions with chain B, 4 interactions with chain A- Hydrophobic interactions: B:I.52, B:I.52, B:W.80, B:W.80, B:W.80, B:F.88, B:L.123, A:L.87, A:I.117, A:L.123, A:V.124
- Hydrogen bonds: B:Y.64
L2P.34: 23 residues within 4Å:- Chain A: G.21, T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, A.51, F.54, T.55
- Chain C: T.107, A.110, A.114, I.117, I.140, A.143, A.144, Y.147
- Ligands: D10.4, HP6.5, UND.48
7 PLIP interactions:4 interactions with chain A, 3 interactions with chain C- Hydrophobic interactions: A:L.25, A:L.28, A:T.47, A:L.48, C:A.110, C:Y.147, C:Y.147
L2P.42: 10 residues within 4Å:- Chain C: Y.131, F.135, W.138, A.139, T.142, A.143, L.146, L.190, A.196
- Ligands: UND.41
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:F.135
L2P.43: 28 residues within 4Å:- Chain B: L.87, V.112, G.113, G.116, I.117, G.120, T.121, L.123, V.124, L.127
- Chain C: L.48, I.52, T.55, M.56, Y.64, T.67, W.80, Y.83, A.84, L.87, F.88, L.92, L.123, L.127
- Ligands: L2P.11, L2P.27, C14.30, C14.46
12 PLIP interactions:8 interactions with chain C, 4 interactions with chain B- Hydrophobic interactions: C:I.52, C:I.52, C:W.80, C:W.80, C:W.80, C:F.88, C:L.123, B:L.87, B:I.117, B:L.123, B:V.124
- Hydrogen bonds: C:Y.64
- 3 x TRD: TRIDECANE(Non-covalent)
TRD.3: 13 residues within 4Å:- Chain A: W.138, T.142, M.145, L.146, L.149, Y.150, F.153, F.154, V.179, S.183, P.186, V.187
- Ligands: OCT.7
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:L.146, A:L.149
TRD.19: 13 residues within 4Å:- Chain B: W.138, T.142, M.145, L.146, L.149, Y.150, F.153, F.154, V.179, S.183, P.186, V.187
- Ligands: OCT.23
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:L.146, B:L.149
TRD.35: 13 residues within 4Å:- Chain C: W.138, T.142, M.145, L.146, L.149, Y.150, F.153, F.154, V.179, S.183, P.186, V.187
- Ligands: OCT.39
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:L.146, C:L.149
- 3 x D10: DECANE(Non-covalent)
D10.4: 12 residues within 4Å:- Chain A: W.10, A.14, T.17, A.18, G.21, L.22, L.25, F.54, L.58, L.61
- Ligands: HP6.5, L2P.34
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:T.17, A:L.22
D10.20: 12 residues within 4Å:- Chain B: W.10, A.14, T.17, A.18, G.21, L.22, L.25, F.54, L.58, L.61
- Ligands: L2P.2, HP6.21
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:T.17, B:L.22
D10.36: 12 residues within 4Å:- Chain C: W.10, A.14, T.17, A.18, G.21, L.22, L.25, F.54, L.58, L.61
- Ligands: L2P.18, HP6.37
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:T.17, C:L.22
- 3 x HP6: HEPTANE(Non-functional Binders)
HP6.5: 10 residues within 4Å:- Chain A: I.4, T.17, F.54, L.58, L.61, L.62
- Chain C: V.136, I.140
- Ligands: D10.4, L2P.34
No protein-ligand interaction detected (PLIP)HP6.21: 10 residues within 4Å:- Chain A: V.136, I.140
- Chain B: I.4, T.17, F.54, L.58, L.61, L.62
- Ligands: L2P.2, D10.20
No protein-ligand interaction detected (PLIP)HP6.37: 10 residues within 4Å:- Chain B: V.136, I.140
- Chain C: I.4, T.17, F.54, L.58, L.61, L.62
- Ligands: L2P.18, D10.36
No protein-ligand interaction detected (PLIP)- 9 x OCT: N-OCTANE(Non-covalent)
OCT.6: 6 residues within 4Å:- Chain A: K.172, V.173, N.176, V.177, V.180
- Ligands: DD9.13
No protein-ligand interaction detected (PLIP)OCT.7: 7 residues within 4Å:- Chain A: V.179, V.180, S.183, A.184, V.187
- Ligands: TRD.3, MYS.8
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:V.179
OCT.15: 5 residues within 4Å:- Chain A: L.22, L.25, Y.26, V.29, K.30
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.26, A:Y.26, A:V.29
OCT.22: 6 residues within 4Å:- Chain B: K.172, V.173, N.176, V.177, V.180
- Ligands: DD9.29
No protein-ligand interaction detected (PLIP)OCT.23: 7 residues within 4Å:- Chain B: V.179, V.180, S.183, A.184, V.187
- Ligands: TRD.19, MYS.24
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:V.179
OCT.31: 5 residues within 4Å:- Chain B: L.22, L.25, Y.26, V.29, K.30
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Y.26, B:Y.26, B:V.29
OCT.38: 6 residues within 4Å:- Chain C: K.172, V.173, N.176, V.177, V.180
- Ligands: DD9.45
No protein-ligand interaction detected (PLIP)OCT.39: 7 residues within 4Å:- Chain C: V.179, V.180, S.183, A.184, V.187
- Ligands: TRD.35, MYS.40
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:V.179
OCT.47: 5 residues within 4Å:- Chain C: L.22, L.25, Y.26, V.29, K.30
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:Y.26, C:Y.26, C:V.29
- 6 x MYS: PENTADECANE(Non-covalent)
MYS.8: 10 residues within 4Å:- Chain A: A.184, V.187, V.188, I.191, I.198, V.199, P.200, I.203, L.207
- Ligands: OCT.7
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:I.191
MYS.12: 11 residues within 4Å:- Chain A: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221, R.225
- Ligands: DD9.13
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.26, A:V.213, A:V.217
MYS.24: 10 residues within 4Å:- Chain B: A.184, V.187, V.188, I.191, I.198, V.199, P.200, I.203, L.207
- Ligands: OCT.23
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:I.191
MYS.28: 11 residues within 4Å:- Chain B: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221, R.225
- Ligands: DD9.29
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:Y.26, B:V.213, B:V.217
MYS.40: 10 residues within 4Å:- Chain C: A.184, V.187, V.188, I.191, I.198, V.199, P.200, I.203, L.207
- Ligands: OCT.39
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:I.191
MYS.44: 11 residues within 4Å:- Chain C: L.19, L.22, G.23, Y.26, V.213, S.214, V.217, G.218, L.221, R.225
- Ligands: DD9.45
3 PLIP interactions:3 interactions with chain C- Hydrophobic interactions: C:Y.26, C:V.213, C:V.217
- 6 x UND: UNDECANE(Non-covalent)
UND.9: 6 residues within 4Å:- Chain A: Y.131, S.132, F.135, V.136, A.139
- Ligands: L2P.10
2 PLIP interactions:2 interactions with chain A- Hydrophobic interactions: A:Y.131, A:A.139
UND.16: 7 residues within 4Å:- Chain A: A.143, L.146, Y.147, Y.150
- Chain B: L.28, M.32
- Ligands: L2P.2
1 PLIP interactions:1 interactions with chain A- Hydrophobic interactions: A:Y.150
UND.25: 6 residues within 4Å:- Chain B: Y.131, S.132, F.135, V.136, A.139
- Ligands: L2P.26
2 PLIP interactions:2 interactions with chain B- Hydrophobic interactions: B:Y.131, B:A.139
UND.32: 7 residues within 4Å:- Chain B: A.143, L.146, Y.147, Y.150
- Chain C: L.28, M.32
- Ligands: L2P.18
1 PLIP interactions:1 interactions with chain B- Hydrophobic interactions: B:Y.150
UND.41: 6 residues within 4Å:- Chain C: Y.131, S.132, F.135, V.136, A.139
- Ligands: L2P.42
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:Y.131, C:A.139
UND.48: 7 residues within 4Å:- Chain A: L.28, M.32
- Chain C: A.143, L.146, Y.147, Y.150
- Ligands: L2P.34
1 PLIP interactions:1 interactions with chain C- Hydrophobic interactions: C:Y.150
- 3 x DD9: nonane(Non-covalent)
DD9.13: 9 residues within 4Å:- Chain A: V.177, L.181, S.214, G.218, L.221, I.222, R.225
- Ligands: OCT.6, MYS.12
No protein-ligand interaction detected (PLIP)DD9.29: 9 residues within 4Å:- Chain B: V.177, L.181, S.214, G.218, L.221, I.222, R.225
- Ligands: OCT.22, MYS.28
No protein-ligand interaction detected (PLIP)DD9.45: 9 residues within 4Å:- Chain C: V.177, L.181, S.214, G.218, L.221, I.222, R.225
- Ligands: OCT.38, MYS.44
No protein-ligand interaction detected (PLIP)- 3 x C14: TETRADECANE(Non-covalent)
C14.14: 11 residues within 4Å:- Chain A: L.87, F.88, P.91, L.92, L.95, I.108, L.109, V.112
- Chain B: F.88
- Ligands: L2P.11, L2P.27
4 PLIP interactions:4 interactions with chain A- Hydrophobic interactions: A:L.87, A:P.91, A:L.95, A:I.108
C14.30: 11 residues within 4Å:- Chain B: L.87, F.88, P.91, L.92, L.95, I.108, L.109, V.112
- Chain C: F.88
- Ligands: L2P.27, L2P.43
4 PLIP interactions:4 interactions with chain B- Hydrophobic interactions: B:L.87, B:P.91, B:L.95, B:I.108
C14.46: 11 residues within 4Å:- Chain A: F.88
- Chain C: L.87, F.88, P.91, L.92, L.95, I.108, L.109, V.112
- Ligands: L2P.11, L2P.43
4 PLIP interactions:4 interactions with chain C- Hydrophobic interactions: C:L.87, C:P.91, C:L.95, C:I.108
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Nango, E. et al., A three-dimensional movie of structural changes in bacteriorhodopsin. Science (2016)
- Release Date
- 2016-12-21
- Peptides
- Bacteriorhodopsin: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
A - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x RET: RETINAL(Covalent)
- 9 x L2P: 2,3-DI-PHYTANYL-GLYCEROL(Non-covalent)
- 3 x TRD: TRIDECANE(Non-covalent)
- 3 x D10: DECANE(Non-covalent)
- 3 x HP6: HEPTANE(Non-functional Binders)
- 9 x OCT: N-OCTANE(Non-covalent)
- 6 x MYS: PENTADECANE(Non-covalent)
- 6 x UND: UNDECANE(Non-covalent)
- 3 x DD9: nonane(Non-covalent)
- 3 x C14: TETRADECANE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Nango, E. et al., A three-dimensional movie of structural changes in bacteriorhodopsin. Science (2016)
- Release Date
- 2016-12-21
- Peptides
- Bacteriorhodopsin: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
AC
A - Membrane
-
We predict this structure to be a membrane protein.