SMTL ID : 6rqp.1

Steady-state-SMX dark state structure of bacteriorhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 19 residues within 4Å: Chain A: Y.79, W.82, T.85, T.86, L.89, M.114, I.115, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:T.86, A:L.89, A:M.141, A:W.178, A:W.178, A:Y.181, A:Y.181, A:Y.181, A:Y.181, A:P.182, A:A.211, A:K.212 RET.9: 19 residues within 4Å: Chain B: Y.79, W.82, T.85, T.86, L.89, M.114, I.115, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:T.86, B:L.89, B:M.141, B:W.178, B:W.178, B:Y.181, B:Y.181, B:Y.181, B:Y.181, B:P.182, B:A.211, B:K.212 RET.17: 19 residues within 4Å: Chain C: Y.79, W.82, T.85, T.86, L.89, M.114, I.115, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:T.86, C:L.89, C:M.141, C:W.178, C:W.178, C:Y.181, C:Y.181, C:Y.181, C:Y.181, C:P.182, C:A.211, C:K.212

12 x LI1: 1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL(Non-covalent)

LI1.2: 8 residues within 4Å: Chain A: A.10, T.13, A.14, G.17, L.18, F.50, L.57 Ligands: OLC.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.18, A:L.57 LI1.3: 9 residues within 4Å: Chain C: T.63, W.76, A.80, L.83, F.84, L.119, L.123 Ligands: OLC.7, OLC.23 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.76, C:W.76, C:W.76 LI1.4: 1 residues within 4Å: Chain A: F.150 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.150 LI1.5: 6 residues within 4Å: Chain A: F.149, V.175, V.176, S.179, A.180, V.183 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.149, A:V.176, A:A.180 LI1.10: 8 residues within 4Å: Chain B: A.10, T.13, A.14, G.17, L.18, F.50, L.57 Ligands: OLC.14 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.18, B:L.57 LI1.11: 9 residues within 4Å: Chain A: T.63, W.76, A.80, L.83, F.84, L.119, L.123 Ligands: OLC.7, OLC.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.76, A:W.76, A:W.76 LI1.12: 1 residues within 4Å: Chain B: F.150 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.150 LI1.13: 6 residues within 4Å: Chain B: F.149, V.175, V.176, S.179, A.180, V.183 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.149, B:V.176, B:A.180 LI1.18: 8 residues within 4Å: Chain C: A.10, T.13, A.14, G.17, L.18, F.50, L.57 Ligands: OLC.22 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.18, C:L.57 LI1.19: 9 residues within 4Å: Chain B: T.63, W.76, A.80, L.83, F.84, L.119, L.123 Ligands: OLC.15, OLC.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.76, B:W.76, B:W.76 LI1.20: 1 residues within 4Å: Chain C: F.150 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.150 LI1.21: 6 residues within 4Å: Chain C: F.149, V.175, V.176, S.179, A.180, V.183 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.149, C:V.176, C:A.180

9 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.6: 23 residues within 4Å: Chain A: G.17, L.18, T.20, L.21, L.24, K.36, Y.39, A.40, T.43, L.44, A.47, F.50, T.51 Chain C: G.102, T.103, A.106, A.110, I.113, I.136, A.139, A.140, Y.143 Ligands: LI1.2 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain A Hydrophobic interactions: C:A.106, C:Y.143, A:L.21, A:L.24, A:T.43, A:L.44, A:F.50 Hydrogen bonds: C:T.103, A:K.36 OLC.7: 22 residues within 4Å: Chain A: L.44, I.48, T.51, M.52, Y.60, T.63, W.76, A.80, F.84, L.88 Chain C: L.105, V.108, G.109, G.112, I.113, G.116, T.117, L.119, V.120, L.123 Ligands: LI1.3, LI1.11 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:L.105, C:I.113, C:V.120, A:I.48, A:I.48, A:W.76, A:L.88 OLC.8: 4 residues within 4Å: Chain A: I.199, L.202, L.203, V.206 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.202, A:V.206 OLC.14: 23 residues within 4Å: Chain A: G.102, T.103, A.106, A.110, I.113, I.136, A.139, A.140, Y.143 Chain B: G.17, L.18, T.20, L.21, L.24, K.36, Y.39, A.40, T.43, L.44, A.47, F.50, T.51 Ligands: LI1.10 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.21, B:L.24, B:T.43, B:L.44, B:F.50, A:A.106, A:Y.143 Hydrogen bonds: B:K.36, A:T.103 OLC.15: 22 residues within 4Å: Chain A: L.105, V.108, G.109, G.112, I.113, G.116, T.117, L.119, V.120, L.123 Chain B: L.44, I.48, T.51, M.52, Y.60, T.63, W.76, A.80, F.84, L.88 Ligands: LI1.11, LI1.19 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.48, B:I.48, B:W.76, B:L.88, A:L.105, A:I.113, A:V.120 OLC.16: 4 residues within 4Å: Chain B: I.199, L.202, L.203, V.206 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.202, B:V.206 OLC.22: 23 residues within 4Å: Chain B: G.102, T.103, A.106, A.110, I.113, I.136, A.139, A.140, Y.143 Chain C: G.17, L.18, T.20, L.21, L.24, K.36, Y.39, A.40, T.43, L.44, A.47, F.50, T.51 Ligands: LI1.18 9 PLIP interactions: 6 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.21, C:L.24, C:T.43, C:L.44, C:F.50, B:A.106, B:Y.143 Hydrogen bonds: C:K.36, B:T.103 OLC.23: 22 residues within 4Å: Chain B: L.105, V.108, G.109, G.112, I.113, G.116, T.117, L.119, V.120, L.123 Chain C: L.44, I.48, T.51, M.52, Y.60, T.63, W.76, A.80, F.84, L.88 Ligands: LI1.3, LI1.19 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.48, C:I.48, C:W.76, C:L.88, B:L.105, B:I.113, B:V.120 OLC.24: 4 residues within 4Å: Chain C: I.199, L.202, L.203, V.206 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.202, C:V.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Weinert, T. et al., Proton uptake mechanism in bacteriorhodopsin captured by serial synchrotron crystallography. Science (2019)

Release Date

2019-07-17

Peptides

Bacteriorhodopsin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin

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