SMTL ID : 7xje.1

Crystal structure of bacteriorhodopsin in the K state refined against the extrapolated dataset

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: Y.79, W.82, T.85, T.86, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.79, A:W.82, A:W.82, A:T.86, A:M.141, A:W.178, A:W.178, A:Y.181, A:Y.181, A:Y.181, A:Y.181, A:W.185, A:A.211, A:K.212 RET.12: 17 residues within 4Å: Chain B: Y.79, W.82, T.85, T.86, 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.79, B:W.82, B:W.82, B:T.86, B:M.141, B:W.178, B:W.178, B:Y.181, B:Y.181, B:Y.181, B:Y.181, B:W.185, B:A.211, B:K.212 RET.23: 17 residues within 4Å: Chain C: Y.79, W.82, T.85, T.86, 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 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.79, C:W.82, C:W.82, C:T.86, C:M.141, C:W.178, C:W.178, C:Y.181, C:Y.181, C:Y.181, C:Y.181, C:W.185, C:A.211, C:K.212

30 x L2P: 2,3-DI-PHYTANYL-GLYCEROL(Non-covalent)(Non-functional Binders)

L2P.2: 27 residues within 4Å: Chain A: L.44, I.48, T.51, 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: L.83, G.116, L.119 Ligands: L2P.13, L2P.18, L2P.24, L2P.29 Ligand excluded by PLIP L2P.3: 20 residues within 4Å: Chain A: A.106, A.110, A.139, A.140, L.142, Y.143, Y.146 Chain C: G.17, T.20, L.21, L.24, M.28, K.36, Y.39, A.40, T.43, L.44, A.47, F.50 Ligands: L2P.4 Ligand excluded by PLIP L2P.4: 9 residues within 4Å: Chain A: V.132, I.136, A.139 Chain C: A.10, T.13, A.14, G.17, L.18 Ligands: L2P.3 Ligand excluded by PLIP L2P.5: 5 residues within 4Å: Chain A: V.183, I.194, V.195, P.196, L.203 Ligand excluded by PLIP L2P.6: 3 residues within 4Å: Chain A: F.131, W.134, L.186 Ligand excluded by PLIP L2P.7: 12 residues within 4Å: Chain A: L.83, P.87, L.88, L.91, I.104, L.105, V.108 Chain C: F.84 Ligands: L2P.13, L2P.18, L2P.24, L2P.29 Ligand excluded by PLIP L2P.8: 2 residues within 4Å: Chain A: N.172, V.173 Ligand excluded by PLIP L2P.9: 2 residues within 4Å: Chain A: S.128, F.131 Ligand excluded by PLIP L2P.10: 6 residues within 4Å: Chain A: Y.22, S.210, V.213, G.214, L.217, R.221 Ligand excluded by PLIP L2P.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP L2P.13: 27 residues within 4Å: Chain A: L.83, G.116, L.119 Chain B: L.44, I.48, T.51, 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.7, L2P.24, L2P.29 Ligand excluded by PLIP L2P.14: 20 residues within 4Å: Chain A: G.17, T.20, L.21, L.24, M.28, K.36, Y.39, A.40, T.43, L.44, A.47, F.50 Chain B: A.106, A.110, A.139, A.140, L.142, Y.143, Y.146 Ligands: L2P.15 Ligand excluded by PLIP L2P.15: 9 residues within 4Å: Chain A: A.10, T.13, A.14, G.17, L.18 Chain B: V.132, I.136, A.139 Ligands: L2P.14 Ligand excluded by PLIP L2P.16: 5 residues within 4Å: Chain B: V.183, I.194, V.195, P.196, L.203 Ligand excluded by PLIP L2P.17: 3 residues within 4Å: Chain B: F.131, W.134, L.186 Ligand excluded by PLIP L2P.18: 12 residues within 4Å: Chain A: F.84 Chain B: L.83, P.87, L.88, L.91, I.104, L.105, V.108 Ligands: L2P.2, L2P.7, L2P.24, L2P.29 Ligand excluded by PLIP L2P.19: 2 residues within 4Å: Chain B: N.172, V.173 Ligand excluded by PLIP L2P.20: 2 residues within 4Å: Chain B: S.128, F.131 Ligand excluded by PLIP L2P.21: 6 residues within 4Å: Chain B: Y.22, S.210, V.213, G.214, L.217, R.221 Ligand excluded by PLIP L2P.22: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP L2P.24: 27 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: L.83, G.116, L.119 Chain C: L.44, I.48, T.51, M.52, Y.60, W.76, F.84, L.88 Ligands: L2P.2, L2P.7, L2P.13, L2P.18 Ligand excluded by PLIP L2P.25: 20 residues within 4Å: Chain B: G.17, T.20, L.21, L.24, M.28, K.36, Y.39, A.40, T.43, L.44, A.47, F.50 Chain C: A.106, A.110, A.139, A.140, L.142, Y.143, Y.146 Ligands: L2P.26 Ligand excluded by PLIP L2P.26: 9 residues within 4Å: Chain B: A.10, T.13, A.14, G.17, L.18 Chain C: V.132, I.136, A.139 Ligands: L2P.25 Ligand excluded by PLIP L2P.27: 5 residues within 4Å: Chain C: V.183, I.194, V.195, P.196, L.203 Ligand excluded by PLIP L2P.28: 3 residues within 4Å: Chain C: F.131, W.134, L.186 Ligand excluded by PLIP L2P.29: 12 residues within 4Å: Chain B: F.84 Chain C: L.83, P.87, L.88, L.91, I.104, L.105, V.108 Ligands: L2P.2, L2P.7, L2P.13, L2P.18 Ligand excluded by PLIP L2P.30: 2 residues within 4Å: Chain C: N.172, V.173 Ligand excluded by PLIP L2P.31: 2 residues within 4Å: Chain C: S.128, F.131 Ligand excluded by PLIP L2P.32: 6 residues within 4Å: Chain C: Y.22, S.210, V.213, G.214, L.217, R.221 Ligand excluded by PLIP L2P.33: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

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Citation

Taguchi, S. et al., Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin. Commun Biol (2023)

Release Date

2023-03-01

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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