SMTL ID : 5zin.1

Crystal structure of bacteriorhodopsin at 1.27 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.27 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: W.82, T.85, T.86, L.89, M.114, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.86, A:L.89, A:M.141, A:W.178, A:Y.181, A:Y.181, A:Y.181, A:P.182, A:W.185, A:A.211, A:K.212 RET.5: 17 residues within 4Å: Chain B: W.82, T.85, T.86, L.89, M.114, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:T.86, B:L.89, B:M.141, B:W.178, B:Y.181, B:Y.181, B:Y.181, B:P.182, B:W.185, B:A.211, B:K.212 RET.9: 17 residues within 4Å: Chain C: W.82, T.85, T.86, L.89, M.114, G.118, W.134, S.137, T.138, M.141, W.178, Y.181, P.182, W.185, D.208, A.211, K.212 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:T.86, C:L.89, C:M.141, C:W.178, C:Y.181, C:Y.181, C:Y.181, C:P.182, C:W.185, C:A.211, C:K.212

9 x L2P: 2,3-DI-PHYTANYL-GLYCEROL(Non-covalent)

L2P.2: 24 residues within 4Å: Chain A: L.44, I.48, M.52, Y.60, W.76, A.80, F.84, L.88 Chain B: W.76, A.80, L.83, F.84, G.109, G.112, I.113, G.116, L.119, V.120, L.123 Chain C: L.83, G.116, L.119 Ligands: L2P.6, L2P.10 25 PLIP interactions: 11 interactions with chain A, 12 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: A:L.44, A:I.48, A:Y.60, A:W.76, A:A.80, A:F.84, A:F.84, A:F.84, A:F.84, A:L.88, B:W.76, B:W.76, B:W.76, B:A.80, B:L.83, B:F.84, B:F.84, B:I.113, B:L.119, B:L.119, B:V.120, B:L.123, C:L.83, C:L.119 Hydrogen bonds: A:Y.60 L2P.3: 15 residues within 4Å: Chain A: A.106, A.110, I.113, A.140, Y.143, Y.146 Chain C: G.17, T.20, L.24, M.28, A.40, T.43, L.44, A.47, F.50 15 PLIP interactions: 8 interactions with chain C, 7 interactions with chain A Hydrophobic interactions: C:L.24, C:A.40, C:L.44, C:L.44, C:A.47, C:F.50, C:F.50, A:A.110, A:I.113, A:I.113, A:A.140, A:Y.143, A:Y.143 Water bridges: C:G.27 Hydrogen bonds: A:Y.143 L2P.4: 6 residues within 4Å: Chain A: K.168, N.172, V.175, V.176, S.179, V.183 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.172, A:V.175, A:V.176, A:V.183 Hydrogen bonds: A:N.172 L2P.6: 24 residues within 4Å: Chain A: L.83, G.116, L.119 Chain B: L.44, I.48, M.52, Y.60, W.76, A.80, F.84, L.88 Chain C: W.76, A.80, L.83, F.84, G.109, G.112, I.113, G.116, L.119, V.120, L.123 Ligands: L2P.2, L2P.10 25 PLIP interactions: 12 interactions with chain C, 2 interactions with chain A, 11 interactions with chain B Hydrophobic interactions: C:W.76, C:W.76, C:W.76, C:A.80, C:L.83, C:F.84, C:F.84, C:I.113, C:L.119, C:L.119, C:V.120, C:L.123, A:L.83, A:L.119, B:L.44, B:I.48, B:Y.60, B:W.76, B:A.80, B:F.84, B:F.84, B:F.84, B:F.84, B:L.88 Hydrogen bonds: B:Y.60 L2P.7: 15 residues within 4Å: Chain A: G.17, T.20, L.24, M.28, A.40, T.43, L.44, A.47, F.50 Chain B: A.106, A.110, I.113, A.140, Y.143, Y.146 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.24, A:A.40, A:L.44, A:L.44, A:A.47, A:F.50, A:F.50, B:A.110, B:I.113, B:I.113, B:A.140, B:Y.143, B:Y.143 Water bridges: A:G.27 Hydrogen bonds: B:Y.143 L2P.8: 6 residues within 4Å: Chain B: K.168, N.172, V.175, V.176, S.179, V.183 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.172, B:V.175, B:V.176, B:V.183 Hydrogen bonds: B:N.172 L2P.10: 24 residues within 4Å: Chain A: W.76, A.80, L.83, F.84, G.109, G.112, I.113, G.116, L.119, V.120, L.123 Chain B: L.83, G.116, L.119 Chain C: L.44, I.48, M.52, Y.60, W.76, A.80, F.84, L.88 Ligands: L2P.2, L2P.6 25 PLIP interactions: 12 interactions with chain A, 11 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:W.76, A:W.76, A:W.76, A:A.80, A:L.83, A:F.84, A:F.84, A:I.113, A:L.119, A:L.119, A:V.120, A:L.123, C:L.44, C:I.48, C:Y.60, C:W.76, C:A.80, C:F.84, C:F.84, C:F.84, C:F.84, C:L.88, B:L.83, B:L.119 Hydrogen bonds: C:Y.60 L2P.11: 15 residues within 4Å: Chain B: G.17, T.20, L.24, M.28, A.40, T.43, L.44, A.47, F.50 Chain C: A.106, A.110, I.113, A.140, Y.143, Y.146 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:A.110, C:I.113, C:I.113, C:A.140, C:Y.143, C:Y.143, B:L.24, B:A.40, B:L.44, B:L.44, B:A.47, B:F.50, B:F.50 Hydrogen bonds: C:Y.143 Water bridges: B:G.27 L2P.12: 6 residues within 4Å: Chain C: K.168, N.172, V.175, V.176, S.179, V.183 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:N.172, C:V.175, C:V.176, C:V.183 Hydrogen bonds: C:N.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hasegawa, N. et al., X-ray structure analysis of bacteriorhodopsin at 1.3 angstrom resolution. Sci Rep (2018)

Release Date

2018-10-10

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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