SMTL ID : 7xjd.1

Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: W.82, T.85, T.86, L.89, M.114, 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.20: 16 residues within 4Å: Chain B: W.82, T.85, T.86, L.89, M.114, 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.39: 16 residues within 4Å: Chain C: W.82, T.85, T.86, L.89, M.114, 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

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

L2P.2: 27 residues within 4Å: Chain A: I.48, T.51, M.52, Y.60, W.76, A.80, F.84, L.88 Chain B: W.76, A.80, L.83, F.84, L.105, G.109, G.112, I.113, G.116, T.117, L.119, V.120, L.123 Chain C: G.116, L.119 Ligands: L2P.21, L2P.29, L2P.40, L2P.48 Ligand excluded by PLIP L2P.3: 19 residues within 4Å: Chain A: A.106, I.136, A.139, A.140, L.142, Y.143, Y.146 Chain C: G.17, T.20, L.21, L.24, M.28, K.36, A.40, T.43, L.44, F.50 Ligands: L2P.5, L2P.15 Ligand excluded by PLIP L2P.4: 9 residues within 4Å: Chain A: K.168, N.172, V.175, V.176, S.179, A.180 Ligands: L2P.6, L2P.14, SQU.19 Ligand excluded by PLIP L2P.5: 16 residues within 4Å: Chain A: Y.129, V.132, I.136, A.139 Chain C: A.10, T.13, A.14, G.17, L.18, L.54 Ligands: L2P.3, SQU.7, L2P.13, L2P.15, SQU.55, SQU.56 Ligand excluded by PLIP L2P.6: 11 residues within 4Å: Chain A: A.180, V.183, I.187, I.194, V.195, P.196, I.199, L.203, L.207 Ligands: L2P.4, L2P.14 Ligand excluded by PLIP L2P.8: 3 residues within 4Å: Chain A: L.21, Y.22, V.25 Ligand excluded by PLIP L2P.9: 5 residues within 4Å: Chain A: Y.127, F.131, W.134, L.186 Ligands: L2P.12 Ligand excluded by PLIP L2P.10: 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.21, L2P.29, L2P.40, L2P.48 Ligand excluded by PLIP L2P.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP L2P.12: 2 residues within 4Å: Chain A: F.131 Ligands: L2P.9 Ligand excluded by PLIP L2P.13: 4 residues within 4Å: Chain A: V.132 Ligands: L2P.5, SQU.7, SQU.55 Ligand excluded by PLIP L2P.14: 6 residues within 4Å: Chain A: N.172, V.173, V.176, L.177 Ligands: L2P.4, L2P.6 Ligand excluded by PLIP L2P.15: 4 residues within 4Å: Chain A: A.135, A.139 Ligands: L2P.3, L2P.5 Ligand excluded by PLIP L2P.16: 8 residues within 4Å: Chain A: L.15, L.18, Y.22, S.210, V.213, G.214, L.217, R.221 Ligand excluded by PLIP L2P.21: 27 residues within 4Å: Chain A: G.116, L.119 Chain B: I.48, T.51, M.52, Y.60, W.76, A.80, F.84, L.88 Chain C: W.76, A.80, L.83, F.84, L.105, G.109, G.112, I.113, G.116, T.117, L.119, V.120, L.123 Ligands: L2P.2, L2P.10, L2P.40, L2P.48 Ligand excluded by PLIP L2P.22: 19 residues within 4Å: Chain A: G.17, T.20, L.21, L.24, M.28, K.36, A.40, T.43, L.44, F.50 Chain B: A.106, I.136, A.139, A.140, L.142, Y.143, Y.146 Ligands: L2P.24, L2P.34 Ligand excluded by PLIP L2P.23: 9 residues within 4Å: Chain B: K.168, N.172, V.175, V.176, S.179, A.180 Ligands: L2P.25, L2P.33, SQU.38 Ligand excluded by PLIP L2P.24: 16 residues within 4Å: Chain A: A.10, T.13, A.14, G.17, L.18, L.54 Chain B: Y.129, V.132, I.136, A.139 Ligands: SQU.17, SQU.18, L2P.22, SQU.26, L2P.32, L2P.34 Ligand excluded by PLIP L2P.25: 11 residues within 4Å: Chain B: A.180, V.183, I.187, I.194, V.195, P.196, I.199, L.203, L.207 Ligands: L2P.23, L2P.33 Ligand excluded by PLIP L2P.27: 3 residues within 4Å: Chain B: L.21, Y.22, V.25 Ligand excluded by PLIP L2P.28: 5 residues within 4Å: Chain B: Y.127, F.131, W.134, L.186 Ligands: L2P.31 Ligand excluded by PLIP L2P.29: 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.10, L2P.40, L2P.48 Ligand excluded by PLIP L2P.30: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP L2P.31: 2 residues within 4Å: Chain B: F.131 Ligands: L2P.28 Ligand excluded by PLIP L2P.32: 4 residues within 4Å: Chain B: V.132 Ligands: SQU.17, L2P.24, SQU.26 Ligand excluded by PLIP L2P.33: 6 residues within 4Å: Chain B: N.172, V.173, V.176, L.177 Ligands: L2P.23, L2P.25 Ligand excluded by PLIP L2P.34: 4 residues within 4Å: Chain B: A.135, A.139 Ligands: L2P.22, L2P.24 Ligand excluded by PLIP L2P.35: 8 residues within 4Å: Chain B: L.15, L.18, Y.22, S.210, V.213, G.214, L.217, R.221 Ligand excluded by PLIP L2P.40: 27 residues within 4Å: Chain A: W.76, A.80, L.83, F.84, L.105, G.109, G.112, I.113, G.116, T.117, L.119, V.120, L.123 Chain B: G.116, L.119 Chain C: I.48, T.51, M.52, Y.60, W.76, A.80, F.84, L.88 Ligands: L2P.2, L2P.10, L2P.21, L2P.29 Ligand excluded by PLIP L2P.41: 19 residues within 4Å: Chain B: G.17, T.20, L.21, L.24, M.28, K.36, A.40, T.43, L.44, F.50 Chain C: A.106, I.136, A.139, A.140, L.142, Y.143, Y.146 Ligands: L2P.43, L2P.53 Ligand excluded by PLIP L2P.42: 9 residues within 4Å: Chain C: K.168, N.172, V.175, V.176, S.179, A.180 Ligands: L2P.44, L2P.52, SQU.57 Ligand excluded by PLIP L2P.43: 16 residues within 4Å: Chain B: A.10, T.13, A.14, G.17, L.18, L.54 Chain C: Y.129, V.132, I.136, A.139 Ligands: SQU.36, SQU.37, L2P.41, SQU.45, L2P.51, L2P.53 Ligand excluded by PLIP L2P.44: 11 residues within 4Å: Chain C: A.180, V.183, I.187, I.194, V.195, P.196, I.199, L.203, L.207 Ligands: L2P.42, L2P.52 Ligand excluded by PLIP L2P.46: 3 residues within 4Å: Chain C: L.21, Y.22, V.25 Ligand excluded by PLIP L2P.47: 5 residues within 4Å: Chain C: Y.127, F.131, W.134, L.186 Ligands: L2P.50 Ligand excluded by PLIP L2P.48: 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.10, L2P.21, L2P.29 Ligand excluded by PLIP L2P.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP L2P.50: 2 residues within 4Å: Chain C: F.131 Ligands: L2P.47 Ligand excluded by PLIP L2P.51: 4 residues within 4Å: Chain C: V.132 Ligands: SQU.36, L2P.43, SQU.45 Ligand excluded by PLIP L2P.52: 6 residues within 4Å: Chain C: N.172, V.173, V.176, L.177 Ligands: L2P.42, L2P.44 Ligand excluded by PLIP L2P.53: 4 residues within 4Å: Chain C: A.135, A.139 Ligands: L2P.41, L2P.43 Ligand excluded by PLIP L2P.54: 8 residues within 4Å: Chain C: L.15, L.18, Y.22, S.210, V.213, G.214, L.217, R.221 Ligand excluded by PLIP

12 x SQU: 2,10,23-TRIMETHYL-TETRACOSANE(Non-functional Binders)(Non-covalent)

SQU.7: 2 residues within 4Å: Ligands: L2P.5, L2P.13 No protein-ligand interaction detected (PLIP) SQU.17: 3 residues within 4Å: Ligands: SQU.18, L2P.24, L2P.32 No protein-ligand interaction detected (PLIP) SQU.18: 6 residues within 4Å: Chain A: I.7, L.11, A.14, L.18 Ligands: SQU.17, L2P.24 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.7, A:L.11, A:A.14, A:L.18 SQU.19: 1 residues within 4Å: Ligands: L2P.4 No protein-ligand interaction detected (PLIP) SQU.26: 2 residues within 4Å: Ligands: L2P.24, L2P.32 No protein-ligand interaction detected (PLIP) SQU.36: 3 residues within 4Å: Ligands: SQU.37, L2P.43, L2P.51 No protein-ligand interaction detected (PLIP) SQU.37: 6 residues within 4Å: Chain B: I.7, L.11, A.14, L.18 Ligands: SQU.36, L2P.43 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.7, B:L.11, B:A.14, B:L.18 SQU.38: 1 residues within 4Å: Ligands: L2P.23 No protein-ligand interaction detected (PLIP) SQU.45: 2 residues within 4Å: Ligands: L2P.43, L2P.51 No protein-ligand interaction detected (PLIP) SQU.55: 3 residues within 4Å: Ligands: L2P.5, L2P.13, SQU.56 No protein-ligand interaction detected (PLIP) SQU.56: 6 residues within 4Å: Chain C: I.7, L.11, A.14, L.18 Ligands: L2P.5, SQU.55 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.7, C:L.11, C:A.14, C:L.18 SQU.57: 1 residues within 4Å: Ligands: L2P.42 No protein-ligand interaction detected (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

2023-03-22

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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