SMTL ID : 2z55.6 (5 other biounits)

Bacterioruberin in the trimeric structure of archaerhodopsin-2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: Y.88, W.91, T.95, L.98, M.123, G.127, W.143, S.146, F.150, W.187, Y.190, P.191, W.194, D.217, A.220, K.221 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.88, A:T.95, A:L.98, A:F.150, A:F.150, A:W.187, A:W.187, A:Y.190, A:Y.190, A:Y.190, A:Y.190, A:Y.190, A:P.191, A:W.194, A:A.220, A:K.221 RET.4: 16 residues within 4Å: Chain B: Y.88, W.91, T.95, L.98, M.123, G.127, W.143, S.146, F.150, W.187, Y.190, P.191, W.194, D.217, A.220, K.221 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.88, B:T.95, B:L.98, B:F.150, B:F.150, B:W.187, B:W.187, B:Y.190, B:Y.190, B:Y.190, B:Y.190, B:Y.190, B:P.191, B:W.194, B:A.220, B:K.221 RET.7: 16 residues within 4Å: Chain C: Y.88, W.91, T.95, L.98, M.123, G.127, W.143, S.146, F.150, W.187, Y.190, P.191, W.194, D.217, A.220, K.221 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:Y.88, C:T.95, C:L.98, C:F.150, C:F.150, C:W.187, C:W.187, C:Y.190, C:Y.190, C:Y.190, C:Y.190, C:Y.190, C:P.191, C:W.194, C:A.220, C:K.221

3 x 22B: BACTERIORUBERIN(Non-covalent)

22B.2: 21 residues within 4Å: Chain A: V.111, T.112, T.115, V.119, L.122, L.137, T.141, L.144, F.145, Y.156 Chain C: L.6, L.25, T.28, F.29, I.32, G.35, R.44, A.48, I.51, L.52, G.55 16 PLIP interactions: 10 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:V.111, A:T.115, A:V.119, A:L.122, A:L.137, A:T.141, A:L.144, A:F.145, A:Y.156, C:T.28, C:F.29, C:I.32, C:I.51, C:L.52 Hydrogen bonds: A:Y.156, C:R.44 22B.5: 21 residues within 4Å: Chain A: L.6, L.25, T.28, F.29, I.32, G.35, R.44, A.48, I.51, L.52, G.55 Chain B: V.111, T.112, T.115, V.119, L.122, L.137, T.141, L.144, F.145, Y.156 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.111, B:T.115, B:V.119, B:L.122, B:L.137, B:T.141, B:L.144, B:F.145, B:Y.156, A:T.28, A:F.29, A:I.32, A:I.51, A:L.52 Hydrogen bonds: B:Y.156, A:R.44 22B.8: 21 residues within 4Å: Chain B: L.6, L.25, T.28, F.29, I.32, G.35, R.44, A.48, I.51, L.52, G.55 Chain C: V.111, T.112, T.115, V.119, L.122, L.137, T.141, L.144, F.145, Y.156 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain C Hydrophobic interactions: B:T.28, B:F.29, B:I.32, B:I.51, B:L.52, C:V.111, C:T.115, C:V.119, C:L.122, C:L.137, C:T.141, C:L.144, C:F.145, C:Y.156 Hydrogen bonds: B:R.44, C:Y.156

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

L2P.3: 18 residues within 4Å: Chain A: I.56, I.68, Y.85, A.89, F.93, L.97 Chain B: T.71, Y.85, A.89, F.93, G.118, L.122, V.125, I.129, L.132 Chain C: L.92 Ligands: L2P.6, L2P.9 15 PLIP interactions: 8 interactions with chain B, 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:T.71, B:Y.85, B:Y.85, B:A.89, B:F.93, B:L.122, B:V.125, B:V.125, A:I.68, A:Y.85, A:F.93, A:L.97, C:L.92, C:L.92 Hydrogen bonds: A:Y.85 L2P.6: 18 residues within 4Å: Chain A: L.92 Chain B: I.56, I.68, Y.85, A.89, F.93, L.97 Chain C: T.71, Y.85, A.89, F.93, G.118, L.122, V.125, I.129, L.132 Ligands: L2P.3, L2P.9 15 PLIP interactions: 5 interactions with chain B, 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:I.68, B:Y.85, B:F.93, B:L.97, C:T.71, C:Y.85, C:Y.85, C:A.89, C:F.93, C:L.122, C:V.125, C:V.125, A:L.92, A:L.92 Hydrogen bonds: B:Y.85 L2P.9: 18 residues within 4Å: Chain A: T.71, Y.85, A.89, F.93, G.118, L.122, V.125, I.129, L.132 Chain B: L.92 Chain C: I.56, I.68, Y.85, A.89, F.93, L.97 Ligands: L2P.3, L2P.6 15 PLIP interactions: 8 interactions with chain A, 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:T.71, A:Y.85, A:Y.85, A:A.89, A:F.93, A:L.122, A:V.125, A:V.125, C:I.68, C:Y.85, C:F.93, C:L.97, B:L.92, B:L.92 Hydrogen bonds: C:Y.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshimura, K. et al., Structural role of bacterioruberin in the trimeric structure of archaerhodopsin-2. J.Mol.Biol. (2008)

Release Date

2008-01-01

Peptides

Archaerhodopsin-2: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
E

C
E

Membrane

We predict this structure to be a membrane protein.
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Archaerhodopsin-2

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