SMTL ID : 3vvk.2 (1 other biounit)

An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 15 residues within 4Å: Chain A: W.127, T.131, I.134, M.159, G.163, Y.180, S.183, C.184, F.187, W.222, Y.225, P.226, W.229, D.252, K.256 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.127, A:W.127, A:T.131, A:I.134, A:Y.180, A:Y.180, A:F.187, A:F.187, A:W.222, A:Y.225, A:Y.225, A:Y.225, A:Y.225, A:Y.225, A:P.226, A:W.229, A:K.256 RET.5: 14 residues within 4Å: Chain B: W.127, T.131, M.159, G.163, Y.180, S.183, C.184, F.187, W.222, Y.225, P.226, W.229, D.252, K.256 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:W.127, B:W.127, B:T.131, B:Y.180, B:Y.180, B:F.187, B:W.222, B:W.222, B:Y.225, B:Y.225, B:Y.225, B:Y.225, B:P.226, B:W.229, B:K.256 RET.9: 15 residues within 4Å: Chain C: W.127, S.130, T.131, I.134, M.159, G.163, Y.180, S.183, F.187, W.222, Y.225, P.226, W.229, D.252, K.256 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:W.127, C:W.127, C:T.131, C:I.134, C:Y.180, C:Y.180, C:F.187, C:F.187, C:W.222, C:W.222, C:Y.225, C:Y.225, C:Y.225, C:Y.225, C:P.226, C:W.229, C:W.229, C:K.256

2 x L3P: 2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE(Non-covalent)

L3P.2: 9 residues within 4Å: Chain A: A.146, L.149, F.150, I.153, T.154, I.157, A.158, V.161 Chain B: V.77 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.149, A:F.150, A:I.153, A:T.154, A:I.157, A:V.161, B:V.77 L3P.7: 10 residues within 4Å: Chain B: A.146, L.149, F.150, I.153, I.157, A.158, V.161 Chain C: V.77, L.129, M.133 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:V.77, C:L.129, C:L.129, B:L.149, B:F.150, B:F.150, B:I.153, B:I.153, B:I.157, B:V.161

3 x AZI: AZIDE ION(Non-covalent)

AZI.3: 6 residues within 4Å: Chain A: S.78, S.81, T.126, W.127, S.130, K.256 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.78, A:S.81, A:T.126, A:S.130 AZI.8: 7 residues within 4Å: Chain B: V.77, S.78, S.81, T.126, W.127, S.130, K.256 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.81, B:T.126, B:S.130, B:S.130 Water bridges: B:S.81, B:Y.82, B:W.127, B:D.252 AZI.10: 7 residues within 4Å: Chain C: S.78, S.81, T.126, W.127, S.130, D.252, K.256 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.81, C:T.126, C:W.127, C:S.130, C:D.252

1 x BNG: nonyl beta-D-glucopyranoside(Non-covalent)

BNG.4: 3 residues within 4Å: Chain A: G.99, F.101, H.173 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.101 Hydrogen bonds: A:G.99 Salt bridges: A:H.173

1 x 22B: BACTERIORUBERIN(Non-covalent)

22B.6: 13 residues within 4Å: Chain A: K.148, T.151, F.155, A.185, V.189, Y.192, E.197 Chain B: I.49, L.50, V.53, T.56, K.65, A.68 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.49, B:L.50, B:V.53, B:K.65, B:A.68, A:K.148, A:F.155, A:F.155, A:A.185, A:V.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakanishi, T. et al., Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide. Biophys.J. (2013)

Release Date

2013-06-19

Peptides

Halorhodopsin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
E

C
F

Membrane

We predict this structure to be a membrane protein.
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Halorhodopsin

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