SMTL ID : 5ite.1

2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi Bacteriorhodopsin (HwBR) from Octylglucoside (OG) Detergent Micelles

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 18 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, D.220, A.223, K.224 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.91, A:W.94, A:T.98, A:L.101, A:M.153, 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.4: 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 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.91, B:W.94, 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:Y.193, B:Y.193, B:P.194, B:W.197, B:A.223, B:K.224 RET.9: 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:M.153, C:W.190, 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

3 x OLB: (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLB.2: 12 residues within 4Å: Chain A: I.122, S.152, F.155, Y.159 Chain C: M.31, I.35, V.51, I.54, L.55, A.58, A.61, A.62 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.54, C:L.55, C:A.58, C:A.61, A:I.122, A:I.122 Salt bridges: C:K.47 Hydrogen bonds: A:Y.159 OLB.8: 12 residues within 4Å: Chain B: T.24, L.28, M.31, I.54, L.55, A.61, L.65 Chain C: I.122, F.125, I.148, I.151, Y.159 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain C Hydrophobic interactions: B:T.24, B:I.54, B:L.55, B:A.61, B:L.65, C:I.122, C:F.125, C:F.125, C:I.148, C:I.148, C:I.151 Hydrogen bonds: C:Y.159 OLB.12: 14 residues within 4Å: Chain A: Q.113, R.114, G.117, G.121, A.124, F.125, V.128 Chain C: I.59, S.63, S.66, F.96, L.100, L.103 Ligands: OLC.10 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.59, C:F.96, C:F.96, C:L.103, A:A.124, A:V.128, A:V.128

6 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.3: 6 residues within 4Å: Chain A: P.99, L.103, L.107, Q.113, I.116 Ligands: OLC.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:P.99, A:L.103, A:L.107, A:I.116 OLC.5: 20 residues within 4Å: Chain A: E.48, V.51, L.55, I.59, A.62, A.89, A.92, F.96, L.100, L.103 Chain B: R.114, G.117, A.118, G.121, A.124, F.125, V.128, V.132 Ligands: OLC.3, OLC.6 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.59, A:I.59, A:A.62, A:A.89, A:A.92, A:F.96, A:L.100, B:A.124, B:F.125, B:V.128, B:V.132 Hydrogen bonds: A:E.48, A:E.48 OLC.6: 13 residues within 4Å: Chain A: F.96 Chain B: L.95, F.96, P.99, L.100, L.103, L.107, A.111, S.112, Q.113, I.116, A.124 Ligands: OLC.5 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.96, B:P.99, B:L.100, B:L.103, B:L.103, B:I.116, B:A.124, A:F.96 Hydrogen bonds: B:A.111 OLC.7: 5 residues within 4Å: Chain B: L.157, Y.158, V.161, L.187, A.191 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.157, B:L.157, B:Y.158, B:V.161, B:L.187 OLC.10: 11 residues within 4Å: Chain B: F.96 Chain C: L.95, P.99, L.100, L.107, A.111, Q.113, I.116, A.124, V.128 Ligands: OLB.12 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:L.95, C:L.95, C:P.99, C:L.100, C:A.124, C:V.128, B:F.96, B:F.96 Hydrogen bonds: C:A.111, C:Q.113 Water bridges: C:Q.113 OLC.11: 16 residues within 4Å: Chain B: K.47, E.48, V.51, I.52, L.55, I.59, F.96, L.100 Chain C: R.114, D.115, G.117, A.118, G.121, A.124, F.125, V.163 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:E.48, B:V.51, B:I.52, B:L.55, B:I.59, B:I.59, B:F.96, B:F.96, B:F.96, B:L.100, C:R.114, C:A.118, C:A.124 Hydrogen bonds: B:K.47 Salt bridges: B:K.47

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Broecker, J. et al., Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs. Structure (2017)

Release Date

2017-01-25

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.
Show / Hide

Bacteriorhodopsin-I