SMTL ID : 4qi1.1

Crystal structure of H. walsbyi bacteriorhodopsin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: Y.91, W.94, T.97, T.98, L.101, M.126, G.130, W.146, S.149, T.150, M.153, W.190, Y.193, P.194, W.197, A.223, K.224 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.91, A:W.94, A:W.94, A:T.98, A:M.153, A:W.190, A:Y.193, A:Y.193, A:Y.193, A:Y.193, A:P.194, A:W.197, A:A.223, A:K.224 RET.6: 18 residues within 4Å: Chain B: Y.91, W.94, T.97, T.98, L.101, M.126, G.130, W.146, S.149, T.150, M.153, W.190, Y.193, P.194, W.197, D.220, A.223, K.224 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.91, B:W.94, B:T.98, B:L.101, B:M.153, B:W.190, B:Y.193, B:Y.193, B:Y.193, B:P.194, B:W.197, B:A.223, B:K.224 RET.12: 18 residues within 4Å: Chain C: Y.91, W.94, T.97, T.98, L.101, M.126, G.130, W.146, S.149, T.150, M.153, W.190, Y.193, P.194, W.197, D.220, A.223, K.224 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.91, C:T.98, C:L.101, C:M.153, C:W.190, C:Y.193, C:Y.193, C:Y.193, C:Y.193, C:P.194, C:W.197, C:A.223, C:K.224

9 x MPG: [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate(Non-covalent)

MPG.2: 10 residues within 4Å: Chain A: L.95, F.96, L.103, A.111, Q.113, I.116, A.124 Chain C: F.96 Ligands: MPG.4, MPG.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.96, A:L.103, A:I.116 MPG.3: 17 residues within 4Å: Chain A: M.31, I.35, G.38, L.39, K.47, Y.50, V.51, I.54, L.55, A.58, A.61, A.62 Chain B: I.122, F.125, I.148, S.152, Y.159 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.51, A:I.54, A:L.55, A:A.58, A:A.61, B:I.122, B:F.125, B:F.125, B:F.125, B:I.148 Hydrogen bonds: A:G.38, A:G.38 MPG.4: 19 residues within 4Å: Chain A: R.114, D.115, G.117, A.118, G.121, A.124, F.125, V.128 Chain C: K.47, E.48, V.51, I.52, L.55, I.59, A.62, F.96, L.100 Ligands: MPG.2, MPG.13 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:A.124, A:V.128, C:I.52, C:L.55, C:A.62, C:F.96, C:L.100, C:L.100 Hydrogen bonds: A:D.115, A:A.118 MPG.7: 19 residues within 4Å: Chain B: E.48, V.51, I.52, L.55, I.59, A.62, S.63, S.66, A.89, F.96, L.100, L.103 Chain C: R.114, G.117, G.121, A.124, F.125, V.128, V.132 15 PLIP interactions: 8 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:L.55, B:I.59, B:I.59, B:A.62, B:A.89, B:F.96, B:L.100, C:A.124, C:F.125, C:V.128, C:V.132 Hydrogen bonds: B:E.48, C:R.114 Water bridges: C:R.114, C:D.115 MPG.8: 10 residues within 4Å: Chain A: F.71, F.96 Chain B: T.74, W.88, A.92, L.95, L.131, L.135, T.136, K.137 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:T.74, B:W.88, B:W.88, B:A.92, B:K.137, A:F.71 MPG.9: 7 residues within 4Å: Chain A: L.39 Chain B: T.147, I.151, V.154, F.155, Y.158, Y.159 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.151, B:F.155, B:F.155 Hydrogen bonds: B:Y.159, A:L.39 MPG.10: 5 residues within 4Å: Chain B: V.154, L.157, Y.158, V.161, E.166 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.158, B:Y.158, B:V.161 MPG.11: 14 residues within 4Å: Chain B: T.24, M.31, G.38, L.39, Y.50, I.54, L.55, A.61, A.62 Chain C: I.122, F.125, I.151, S.152, Y.159 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:T.24, B:I.54, B:L.55, B:A.61, C:I.122, C:F.125, C:I.151, C:Y.159 Hydrogen bonds: B:G.38, C:Y.159 MPG.13: 9 residues within 4Å: Chain C: F.96, P.99, S.112, Q.113, R.114, I.116, V.120 Ligands: MPG.2, MPG.4 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Q.113, C:I.116, C:V.120

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 2 residues within 4Å: Chain A: E.14, Y.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.14 Water bridges: A:Y.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsu, M.F. et al., Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity. J. Biol. Chem. (2015)

Release Date

2015-07-29

Peptides

Bacteriorhodopsin-I: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Bacteriorhodopsin-I

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