SMTL ID : 1kgb.1

structure of ground-state bacteriorhodopsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 14 residues within 4Å: Chain A: W.86, T.90, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.86, A:T.90, A:M.145, A:W.182, A:Y.185, A:Y.185, A:Y.185, A:Y.185, A:W.189, A:A.215, A:K.216 RET.15: 14 residues within 4Å: Chain B: W.86, T.90, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.86, B:T.90, B:M.145, B:W.182, B:Y.185, B:Y.185, B:Y.185, B:Y.185, B:W.189, B:A.215, B:K.216 RET.29: 14 residues within 4Å: Chain C: W.86, T.90, M.118, W.138, S.141, T.142, M.145, W.182, Y.185, P.186, W.189, D.212, A.215, K.216 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:W.86, C:T.90, C:M.145, C:W.182, C:Y.185, C:Y.185, C:Y.185, C:Y.185, C:W.189, C:A.215, C:K.216

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

LI1.2: 8 residues within 4Å: Chain A: A.139, I.140, A.143 Chain B: L.58 Ligands: LI1.3, LI1.14, LI1.22, LI1.26 Ligand excluded by PLIP LI1.3: 8 residues within 4Å: Chain A: Y.131, F.135, W.138, A.139, A.196 Ligands: LI1.2, LI1.7, LI1.14 Ligand excluded by PLIP LI1.4: 3 residues within 4Å: Chain A: L.146, F.154 Ligands: LI1.7 Ligand excluded by PLIP LI1.5: 9 residues within 4Å: Chain A: F.153, K.172, N.176, V.179, V.180, S.183, A.184, V.187 Ligands: LI1.10 Ligand excluded by PLIP LI1.6: 5 residues within 4Å: Chain A: L.22, L.25, Y.26, V.29 Ligands: LI1.12 Ligand excluded by PLIP LI1.7: 6 residues within 4Å: Chain A: T.142, L.190, A.196, I.198 Ligands: LI1.3, LI1.4 Ligand excluded by PLIP LI1.8: 14 residues within 4Å: Chain A: T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, F.54 Chain C: A.110, A.114, A.144, Y.147 Ligands: LI1.30 Ligand excluded by PLIP LI1.9: 5 residues within 4Å: Chain A: L.87, F.88, P.91, L.95, V.112 Ligand excluded by PLIP LI1.10: 2 residues within 4Å: Chain A: I.198 Ligands: LI1.5 Ligand excluded by PLIP LI1.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.12: 6 residues within 4Å: Chain A: A.14, A.18, L.22, L.61 Ligands: LI1.6, LI1.30 Ligand excluded by PLIP LI1.13: 15 residues within 4Å: Chain A: M.56, Y.64, W.80, F.88 Chain C: W.80, A.84, F.88, G.116, I.117, G.120, L.123, V.124, L.127 Ligands: LI1.27, LI1.41 Ligand excluded by PLIP LI1.14: 4 residues within 4Å: Chain A: A.139, L.146 Ligands: LI1.2, LI1.3 Ligand excluded by PLIP LI1.16: 8 residues within 4Å: Chain B: A.139, I.140, A.143 Chain C: L.58 Ligands: LI1.17, LI1.28, LI1.36, LI1.40 Ligand excluded by PLIP LI1.17: 8 residues within 4Å: Chain B: Y.131, F.135, W.138, A.139, A.196 Ligands: LI1.16, LI1.21, LI1.28 Ligand excluded by PLIP LI1.18: 3 residues within 4Å: Chain B: L.146, F.154 Ligands: LI1.21 Ligand excluded by PLIP LI1.19: 9 residues within 4Å: Chain B: F.153, K.172, N.176, V.179, V.180, S.183, A.184, V.187 Ligands: LI1.24 Ligand excluded by PLIP LI1.20: 5 residues within 4Å: Chain B: L.22, L.25, Y.26, V.29 Ligands: LI1.26 Ligand excluded by PLIP LI1.21: 6 residues within 4Å: Chain B: T.142, L.190, A.196, I.198 Ligands: LI1.17, LI1.18 Ligand excluded by PLIP LI1.22: 14 residues within 4Å: Chain A: A.110, A.114, A.144, Y.147 Chain B: T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, F.54 Ligands: LI1.2 Ligand excluded by PLIP LI1.23: 5 residues within 4Å: Chain B: L.87, F.88, P.91, L.95, V.112 Ligand excluded by PLIP LI1.24: 2 residues within 4Å: Chain B: I.198 Ligands: LI1.19 Ligand excluded by PLIP LI1.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.26: 6 residues within 4Å: Chain B: A.14, A.18, L.22, L.61 Ligands: LI1.2, LI1.20 Ligand excluded by PLIP LI1.27: 15 residues within 4Å: Chain A: W.80, A.84, F.88, G.116, I.117, G.120, L.123, V.124, L.127 Chain B: M.56, Y.64, W.80, F.88 Ligands: LI1.13, LI1.41 Ligand excluded by PLIP LI1.28: 4 residues within 4Å: Chain B: A.139, L.146 Ligands: LI1.16, LI1.17 Ligand excluded by PLIP LI1.30: 8 residues within 4Å: Chain A: L.58 Chain C: A.139, I.140, A.143 Ligands: LI1.8, LI1.12, LI1.31, LI1.42 Ligand excluded by PLIP LI1.31: 8 residues within 4Å: Chain C: Y.131, F.135, W.138, A.139, A.196 Ligands: LI1.30, LI1.35, LI1.42 Ligand excluded by PLIP LI1.32: 3 residues within 4Å: Chain C: L.146, F.154 Ligands: LI1.35 Ligand excluded by PLIP LI1.33: 9 residues within 4Å: Chain C: F.153, K.172, N.176, V.179, V.180, S.183, A.184, V.187 Ligands: LI1.38 Ligand excluded by PLIP LI1.34: 5 residues within 4Å: Chain C: L.22, L.25, Y.26, V.29 Ligands: LI1.40 Ligand excluded by PLIP LI1.35: 6 residues within 4Å: Chain C: T.142, L.190, A.196, I.198 Ligands: LI1.31, LI1.32 Ligand excluded by PLIP LI1.36: 14 residues within 4Å: Chain B: A.110, A.114, A.144, Y.147 Chain C: T.24, L.25, L.28, K.40, Y.43, A.44, T.47, L.48, F.54 Ligands: LI1.16 Ligand excluded by PLIP LI1.37: 5 residues within 4Å: Chain C: L.87, F.88, P.91, L.95, V.112 Ligand excluded by PLIP LI1.38: 2 residues within 4Å: Chain C: I.198 Ligands: LI1.33 Ligand excluded by PLIP LI1.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LI1.40: 6 residues within 4Å: Chain C: A.14, A.18, L.22, L.61 Ligands: LI1.16, LI1.34 Ligand excluded by PLIP LI1.41: 15 residues within 4Å: Chain B: W.80, A.84, F.88, G.116, I.117, G.120, L.123, V.124, L.127 Chain C: M.56, Y.64, W.80, F.88 Ligands: LI1.13, LI1.27 Ligand excluded by PLIP LI1.42: 4 residues within 4Å: Chain C: A.139, L.146 Ligands: LI1.30, LI1.31 Ligand excluded by PLIP

Links

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Citation

Facciotti, M.T. et al., Structure of an early intermediate in the M-state phase of the bacteriorhodopsin photocycle. Biophys.J. (2001)

Release Date

2001-12-05

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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