- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- homo-pentamer
- Ligands
- 23 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 35 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)
LFA.5: 5 residues within 4Å:- Chain A: N.206, L.210, I.213, I.249, S.253
Ligand excluded by PLIPLFA.6: 2 residues within 4Å:- Chain A: N.140
- Ligands: OLC.12
Ligand excluded by PLIPLFA.7: 1 residues within 4Å:- Chain A: L.223
Ligand excluded by PLIPLFA.8: 0 residues within 4Å:- (No contacts)
Ligand excluded by PLIPLFA.9: 3 residues within 4Å:- Chain A: L.168, G.171, S.175
Ligand excluded by PLIPLFA.13: 11 residues within 4Å:- Chain A: L.40, L.43, I.47, F.72
- Chain E: L.44, I.47, L.48
- Ligands: LFA.16, LFA.57, LFA.71, LFA.72
Ligand excluded by PLIPLFA.16: 9 residues within 4Å:- Chain A: L.44, I.47, L.48
- Chain B: L.43, F.72
- Ligands: LFA.13, LFA.31, LFA.71, LFA.72
Ligand excluded by PLIPLFA.20: 2 residues within 4Å:- Chain B: W.183, K.186
Ligand excluded by PLIPLFA.21: 3 residues within 4Å:- Chain B: W.143, F.144
- Ligands: OLC.2
Ligand excluded by PLIPLFA.22: 4 residues within 4Å:- Chain B: L.212, T.216, L.217
- Ligands: LFA.23
Ligand excluded by PLIPLFA.23: 3 residues within 4Å:- Chain B: S.175, F.179
- Ligands: LFA.22
Ligand excluded by PLIPLFA.24: 5 residues within 4Å:- Chain B: L.168, G.171, A.172, S.175, L.223
Ligand excluded by PLIPLFA.31: 11 residues within 4Å:- Chain B: L.44, I.47, L.48
- Chain C: L.40, I.47, F.72, Y.76
- Ligands: LFA.16, LFA.46, LFA.71, LFA.72
Ligand excluded by PLIPLFA.36: 2 residues within 4Å:- Chain C: W.183, K.186
Ligand excluded by PLIPLFA.37: 4 residues within 4Å:- Chain C: N.206, L.210, I.213, S.253
Ligand excluded by PLIPLFA.38: 6 residues within 4Å:- Chain C: R.139, N.140, F.144, A.147, M.148
- Ligands: OLC.29
Ligand excluded by PLIPLFA.39: 3 residues within 4Å:- Chain C: S.175, F.179
- Ligands: LFA.40
Ligand excluded by PLIPLFA.40: 2 residues within 4Å:- Chain C: T.216
- Ligands: LFA.39
Ligand excluded by PLIPLFA.41: 6 residues within 4Å:- Chain C: L.168, G.171, A.172, S.175, L.223
- Ligands: BOG.43
Ligand excluded by PLIPLFA.46: 7 residues within 4Å:- Chain C: L.44, I.47, L.48
- Chain D: L.43, F.72
- Ligands: LFA.31, LFA.57
Ligand excluded by PLIPLFA.51: 6 residues within 4Å:- Chain D: I.209, L.210, I.213, L.217, L.245, I.249
Ligand excluded by PLIPLFA.52: 8 residues within 4Å:- Chain D: R.139, N.140, W.143, F.144, A.147, M.148, I.151
- Ligands: OLC.49
Ligand excluded by PLIPLFA.53: 2 residues within 4Å:- Chain D: G.220
- Ligands: LFA.55
Ligand excluded by PLIPLFA.54: 7 residues within 4Å:- Chain D: A.41, Y.45, N.264
- Chain E: V.66, L.114
- Ligands: OLC.47, OLC.50
Ligand excluded by PLIPLFA.55: 2 residues within 4Å:- Chain D: T.216
- Ligands: LFA.53
Ligand excluded by PLIPLFA.56: 4 residues within 4Å:- Chain D: L.168, G.171, A.172, S.175
Ligand excluded by PLIPLFA.57: 10 residues within 4Å:- Chain D: L.44, I.47, L.48
- Chain E: I.47, F.72, Y.76
- Ligands: LFA.13, LFA.46, LFA.71, LFA.72
Ligand excluded by PLIPLFA.64: 5 residues within 4Å:- Chain E: N.206, I.209, L.210, I.213, S.253
Ligand excluded by PLIPLFA.65: 1 residues within 4Å:- Ligands: OLC.47
Ligand excluded by PLIPLFA.66: 4 residues within 4Å:- Chain E: L.212, T.216, L.234
- Ligands: LFA.67
Ligand excluded by PLIPLFA.67: 1 residues within 4Å:- Ligands: LFA.66
Ligand excluded by PLIPLFA.68: 2 residues within 4Å:- Chain E: I.173, A.176
Ligand excluded by PLIPLFA.69: 6 residues within 4Å:- Chain E: L.168, G.171, A.172, S.175, P.219, L.223
Ligand excluded by PLIPLFA.71: 5 residues within 4Å:- Ligands: LFA.13, LFA.16, LFA.31, LFA.57, LFA.72
Ligand excluded by PLIPLFA.72: 5 residues within 4Å:- Ligands: LFA.13, LFA.16, LFA.31, LFA.57, LFA.71
Ligand excluded by PLIP- 5 x NA: SODIUM ION(Non-functional Binders)
NA.10: 4 residues within 4Å:- Chain A: Y.25, T.83, F.86
- Chain B: D.102
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:Y.25, A:F.86
- Water bridges: B:D.102
NA.14: 4 residues within 4Å:- Chain A: D.102
- Chain E: Y.25, T.83, F.86
2 PLIP interactions:1 interactions with chain E, 1 interactions with chain A- Hydrogen bonds: E:T.87
- Water bridges: A:D.102
NA.25: 4 residues within 4Å:- Chain B: Y.25, T.83, F.86
- Chain C: D.102
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain B- Water bridges: C:D.102
- Hydrogen bonds: B:F.86
NA.42: 4 residues within 4Å:- Chain C: Y.25, T.83, F.86
- Chain D: D.102
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:Y.25
- Water bridges: C:Y.25, D:D.102
NA.58: 5 residues within 4Å:- Chain D: Y.25, T.83, F.86, T.87
- Chain E: D.102
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:Y.25
- Water bridges: D:F.88
- 5 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
BOG.11: 5 residues within 4Å:- Chain A: L.164, Y.226, V.230, D.231, Y.235
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:L.164
- Hydrogen bonds: A:D.231, A:D.231
BOG.26: 5 residues within 4Å:- Chain B: L.164, Y.226, V.230, D.231, Y.235
3 PLIP interactions:3 interactions with chain B- Hydrophobic interactions: B:L.164, B:V.230
- Hydrogen bonds: B:D.231
BOG.43: 6 residues within 4Å:- Chain C: L.164, Y.226, V.230, D.231, Y.235
- Ligands: LFA.41
2 PLIP interactions:2 interactions with chain C- Hydrophobic interactions: C:L.164
- Hydrogen bonds: C:D.231
BOG.59: 6 residues within 4Å:- Chain D: L.164, L.223, Y.226, V.230, D.231, Y.235
4 PLIP interactions:4 interactions with chain D- Hydrophobic interactions: D:L.164, D:L.223, D:Y.226
- Hydrogen bonds: D:D.231
BOG.70: 5 residues within 4Å:- Chain E: L.164, Y.226, V.230, D.231, Y.235
4 PLIP interactions:4 interactions with chain E- Hydrophobic interactions: E:Y.226
- Hydrogen bonds: E:D.231, E:D.231, E:D.231
- 5 x RET: RETINAL(Covalent)
RET.15: 17 residues within 4Å:- Chain A: Y.110, W.113, D.116, V.117, L.120, M.149, G.153, G.171, S.174, S.175, F.178, W.215, Y.218, P.219, Y.222, S.254, K.255
18 PLIP interactions:18 interactions with chain A- Hydrophobic interactions: A:Y.110, A:W.113, A:W.113, A:D.116, A:V.117, A:F.178, A:F.178, A:W.215, A:W.215, A:Y.218, A:Y.218, A:Y.218, A:Y.218, A:Y.218, A:P.219, A:Y.222, A:Y.222, A:K.255
RET.27: 17 residues within 4Å:- Chain B: Y.110, W.113, D.116, V.117, L.120, M.149, G.153, G.171, S.174, S.175, F.178, W.215, Y.218, P.219, Y.222, S.254, K.255
18 PLIP interactions:18 interactions with chain B- Hydrophobic interactions: B:Y.110, B:W.113, B:W.113, B:D.116, B:V.117, B:F.178, B:F.178, B:W.215, B:W.215, B:Y.218, B:Y.218, B:Y.218, B:Y.218, B:Y.218, B:P.219, B:Y.222, B:Y.222, B:K.255
RET.44: 17 residues within 4Å:- Chain C: Y.110, W.113, D.116, V.117, L.120, M.149, G.153, G.171, S.174, S.175, F.178, W.215, Y.218, P.219, Y.222, S.254, K.255
18 PLIP interactions:18 interactions with chain C- Hydrophobic interactions: C:Y.110, C:W.113, C:W.113, C:D.116, C:V.117, C:F.178, C:F.178, C:W.215, C:W.215, C:Y.218, C:Y.218, C:Y.218, C:Y.218, C:Y.218, C:P.219, C:Y.222, C:Y.222, C:K.255
RET.60: 17 residues within 4Å:- Chain D: Y.110, W.113, D.116, V.117, L.120, M.149, G.153, G.171, S.174, S.175, F.178, W.215, Y.218, P.219, Y.222, S.254, K.255
18 PLIP interactions:18 interactions with chain D- Hydrophobic interactions: D:Y.110, D:W.113, D:W.113, D:D.116, D:V.117, D:F.178, D:F.178, D:W.215, D:W.215, D:Y.218, D:Y.218, D:Y.218, D:Y.218, D:Y.218, D:P.219, D:Y.222, D:Y.222, D:K.255
RET.73: 17 residues within 4Å:- Chain E: Y.110, W.113, D.116, V.117, L.120, M.149, G.153, G.171, S.174, S.175, F.178, W.215, Y.218, P.219, Y.222, S.254, K.255
18 PLIP interactions:18 interactions with chain E- Hydrophobic interactions: E:Y.110, E:W.113, E:W.113, E:D.116, E:V.117, E:F.178, E:F.178, E:W.215, E:W.215, E:Y.218, E:Y.218, E:Y.218, E:Y.218, E:Y.218, E:P.219, E:Y.222, E:Y.222, E:K.255
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kovalev, K. et al., Structure and mechanisms of sodium-pumping KR2 rhodopsin. Sci Adv (2019)
- Release Date
- 2019-04-24
- Peptides
- Sodium pumping rhodopsin: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.80 Å
- Oligo State
- homo-pentamer
- Ligands
- 23 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)
- 35 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)
- 5 x NA: SODIUM ION(Non-functional Binders)
- 5 x BOG: octyl beta-D-glucopyranoside(Non-covalent)
- 5 x RET: RETINAL(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kovalev, K. et al., Structure and mechanisms of sodium-pumping KR2 rhodopsin. Sci Adv (2019)
- Release Date
- 2019-04-24
- Peptides
- Sodium pumping rhodopsin: ABCDE
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
E - Membrane
-
We predict this structure to be a membrane protein.