SMTL ID : 5zim.1

Crystal structure of bacteriorhodopsin at 1.25 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 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 13 PLIP interactions: 13 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:P.182, A:W.185, A:W.185, A:A.211, A:K.212 RET.6: 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 13 PLIP interactions: 13 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:P.182, B:W.185, B:W.185, B:A.211, B:K.212 RET.11: 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 13 PLIP interactions: 13 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:P.182, C:W.185, C:W.185, C:A.211, C:K.212

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

L2P.2: 23 residues within 4Å: Chain A: L.44, I.48, M.52, Y.60, W.76, F.84, L.88 Chain B: W.76, A.80, L.83, F.84, G.109, G.112, I.113, G.116, T.117, L.119, V.120, L.123 Chain C: G.116, L.119 Ligands: L2P.7, L2P.12 17 PLIP interactions: 8 interactions with chain A, 8 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:L.44, A:Y.60, A:W.76, A:W.76, A:F.84, A:F.84, A:L.88, B:W.76, B:A.80, B:L.83, B:F.84, B:I.113, B:L.119, B:V.120, B:L.123, C:L.119 Hydrogen bonds: A:Y.60 L2P.3: 16 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 Ligands: L2P.5 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:A.110, A:I.113, A:A.140, A:Y.143, C:T.20, C:L.44, C:L.44, C:A.47, C:F.50, C:F.50 Hydrogen bonds: A:Y.143 L2P.4: 8 residues within 4Å: Chain A: M.141, F.149, K.168, N.172, V.176, S.179, P.182, V.183 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.149, A:V.176, A:V.176, A:P.182, A:V.183 Hydrogen bonds: A:K.168, A:N.172 L2P.5: 12 residues within 4Å: Chain A: Y.129, V.132, A.135, I.136, A.139 Chain C: A.10, T.13, A.14, G.17, L.18, L.54 Ligands: L2P.3 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:T.13, C:A.14, C:L.18, C:L.54, A:Y.129, A:A.139 Hydrogen bonds: A:Y.129 L2P.7: 23 residues within 4Å: Chain A: G.116, L.119 Chain B: L.44, I.48, M.52, Y.60, W.76, F.84, L.88 Chain C: W.76, A.80, L.83, F.84, G.109, G.112, I.113, G.116, T.117, L.119, V.120, L.123 Ligands: L2P.2, L2P.12 17 PLIP interactions: 8 interactions with chain B, 8 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:L.44, B:Y.60, B:W.76, B:W.76, B:F.84, B:F.84, B:L.88, C:W.76, C:A.80, C:L.83, C:F.84, C:I.113, C:L.119, C:V.120, C:L.123, A:L.119 Hydrogen bonds: B:Y.60 L2P.8: 16 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 Ligands: L2P.10 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:A.110, B:I.113, B:A.140, B:Y.143, A:T.20, A:L.44, A:L.44, A:A.47, A:F.50, A:F.50 Hydrogen bonds: B:Y.143 L2P.9: 8 residues within 4Å: Chain B: M.141, F.149, K.168, N.172, V.176, S.179, P.182, V.183 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.149, B:V.176, B:V.176, B:P.182, B:V.183 Hydrogen bonds: B:K.168, B:N.172 L2P.10: 12 residues within 4Å: Chain A: A.10, T.13, A.14, G.17, L.18, L.54 Chain B: Y.129, V.132, A.135, I.136, A.139 Ligands: L2P.8 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.129, B:A.139, A:T.13, A:A.14, A:L.18, A:L.54 Hydrogen bonds: B:Y.129 L2P.12: 23 residues within 4Å: Chain A: W.76, A.80, L.83, F.84, G.109, G.112, I.113, G.116, T.117, L.119, V.120, L.123 Chain B: G.116, L.119 Chain C: L.44, I.48, M.52, Y.60, W.76, F.84, L.88 Ligands: L2P.2, L2P.7 17 PLIP interactions: 8 interactions with chain A, 8 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:W.76, A:A.80, A:L.83, A:F.84, A:I.113, A:L.119, A:V.120, A:L.123, C:L.44, C:Y.60, C:W.76, C:W.76, C:F.84, C:F.84, C:L.88, B:L.119 Hydrogen bonds: C:Y.60 L2P.13: 16 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 Ligands: L2P.15 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:T.20, B:L.44, B:L.44, B:A.47, B:F.50, B:F.50, C:A.110, C:I.113, C:A.140, C:Y.143 Hydrogen bonds: C:Y.143 L2P.14: 8 residues within 4Å: Chain C: M.141, F.149, K.168, N.172, V.176, S.179, P.182, V.183 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.149, C:V.176, C:V.176, C:P.182, C:V.183 Hydrogen bonds: C:K.168, C:N.172 L2P.15: 12 residues within 4Å: Chain B: A.10, T.13, A.14, G.17, L.18, L.54 Chain C: Y.129, V.132, A.135, I.136, A.139 Ligands: L2P.13 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:T.13, B:A.14, B:L.18, B:L.54, C:Y.129, C:A.139 Hydrogen bonds: C:Y.129

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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