SMTL ID : 5kkh.1

2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Haloquadratum walsbyi (HwBR) at 100 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-trimer

Ligands

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

OLC.1: 22 residues within 4Å: Chain A: E.48, V.51, I.52, L.55, I.59, S.63, S.66, 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.5 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.59, A:I.59, A:I.59, A:A.89, A:A.92, A:F.96, 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, B:A.118 OLC.3: 7 residues within 4Å: Chain A: F.96, P.99, L.103, L.107, Q.113, I.116 Ligands: OLC.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.96, A:P.99, A:P.99, A:L.103, A:L.107 Hydrogen bonds: A:Q.113 OLC.5: 11 residues within 4Å: Chain A: F.96 Chain B: P.99, L.100, L.103, L.107, Q.113, I.116, G.117, A.124 Ligands: OLC.1, OLC.10 9 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:P.99, B:L.100, B:L.103, B:L.103, B:A.124, A:F.96 Hydrogen bonds: B:Q.113 Water bridges: C:Q.113, C:Q.113 OLC.6: 9 residues within 4Å: Chain B: M.153, V.154, L.157, Y.158, V.161, A.162, G.165, E.166, A.191 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.154, B:L.157, B:L.157, B:Y.158, B:V.161, B:A.191 OLC.9: 12 residues within 4Å: Chain B: F.96 Chain C: L.95, P.99, L.100, L.103, L.107, A.111, S.112, Q.113, I.116, A.124 Ligands: OLB.11 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:F.96, B:F.96, C:L.95, C:L.95, C:P.99, C:P.99, C:L.100, C:L.103, C:A.124 Water bridges: C:Q.113 OLC.10: 16 residues within 4Å: Chain B: 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.128 Ligands: OLC.5 11 PLIP interactions: 3 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:A.118, C:A.124, C:V.128, B:V.51, B:I.52, B:L.55, B:I.59, B:I.59, B:F.96, B:F.96, B:L.100

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

OLB.2: 16 residues within 4Å: Chain A: I.122, F.125, I.148, F.155, Y.159 Chain C: T.24, L.28, M.31, I.35, K.47, V.51, I.54, L.55, A.58, A.61, L.65 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:I.122, A:I.122, A:F.125, A:F.125, A:I.148, A:F.155, A:F.155, C:T.24, C:L.28, C:L.28, C:L.55, C:L.65 Hydrogen bonds: A:Y.159 Salt bridges: C:K.47 OLB.7: 16 residues within 4Å: Chain B: T.24, L.28, M.31, I.35, K.47, I.54, L.55, A.58, A.61, A.62, L.65 Chain C: I.122, F.125, I.148, F.155, Y.159 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:I.122, C:F.125, C:I.148, C:I.148, B:L.28, B:L.28, B:I.54, B:L.55, B:A.58, B:L.65 Hydrogen bonds: C:Y.159, B:K.47, B:K.47 Water bridges: C:Y.159, C:Y.159 OLB.11: 17 residues within 4Å: Chain A: R.114, G.117, A.118, G.121, A.124, F.125, V.128 Chain C: E.48, V.51, L.55, I.59, S.63, S.66, F.96, L.100, L.103 Ligands: OLC.9 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:A.124, A:V.128, C:L.55, C:I.59, C:I.59, C:F.96, C:F.96, C:L.103

3 x RET: RETINAL(Covalent)

RET.4: 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.91, A:W.94, A:W.94, A:T.98, A:L.101, A:M.153, A:W.190, A:Y.193, A:Y.193, A:Y.193, A:P.194, A:W.197, A:A.223, A:K.224 RET.8: 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:T.98, B:L.101, B:M.153, B:W.190, 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.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 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.91, C:W.94, C:W.94, C:T.98, C:L.101, C:M.153, C:Y.193, C:Y.193, C:Y.193, C:Y.193, C:P.194, C:W.197, C:A.223, C:K.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Broecker, J. et al., A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals. Cryst Growth Des (2016)

Release Date

2017-02-15

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