SMTL ID : 5etz.1

Structure of the all-trans isomer of pharaonis halorhodopsin in the absence of halide ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: Y.124, W.127, S.130, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.124, A:W.127, A:T.131, A:Y.180, A:F.187, A:W.222, A:Y.225, A:Y.225, A:Y.225, A:Y.225, A:P.226, A:W.229, A:W.229, A:K.256 RET.8: 17 residues within 4Å: Chain B: Y.124, W.127, S.130, T.131, M.159, G.163, Y.180, S.183, C.184, F.187, W.222, Y.225, P.226, W.229, D.252, A.255, K.256 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.124, B:W.127, B:T.131, B:Y.180, B:Y.180, B:F.187, B:F.187, B:W.222, B:Y.225, B:Y.225, B:Y.225, B:Y.225, B:Y.225, B:P.226, B:W.229, B:W.229, B:A.255, B:K.256 RET.13: 18 residues within 4Å: Chain C: Y.124, W.127, S.130, 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, A.255, K.256 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:Y.124, C:W.127, C:T.131, C:I.134, 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:A.255, C:K.256

1 x 22B: BACTERIORUBERIN(Non-covalent)

22B.2: 15 residues within 4Å: Chain A: F.155, A.181, I.182, A.185, V.189, I.193, E.197 Chain B: G.46, I.49, V.53, T.56, V.69, I.72, V.76, I.79 15 PLIP interactions: 9 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:I.49, B:I.49, B:V.53, B:V.69, B:I.72, B:V.76, B:I.79, B:I.79, A:F.155, A:F.155, A:A.181, A:I.182, A:V.189, A:I.193 Water bridges: B:K.65

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

L3P.3: 8 residues within 4Å: Chain A: S.92, V.93, L.94, W.121, L.164, L.168 Ligands: L3P.4, L3P.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.121, A:W.121, A:W.121, A:L.164, A:L.168 L3P.4: 11 residues within 4Å: Chain A: V.77, A.80, L.89, W.121, L.125, L.129 Chain C: T.154, I.157, V.161, A.165 Ligands: L3P.3 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:T.154, C:I.157, C:I.157, C:V.161, C:A.165, A:V.77, A:L.89, A:L.89, A:W.121, A:L.129 L3P.9: 6 residues within 4Å: Chain B: S.92, L.94, W.121, L.168 Ligands: L3P.10, L3P.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.94, B:W.121, B:L.168 L3P.10: 14 residues within 4Å: Chain A: A.158, V.161, T.162, A.165, L.168, W.179 Chain B: V.77, A.80, S.81, G.84, L.89, L.129 Ligands: L3P.3, L3P.9 10 PLIP interactions: 3 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:L.89, B:L.89, B:L.129, A:A.158, A:V.161, A:V.161, A:T.162, A:A.165, A:L.168, A:W.179 L3P.14: 17 residues within 4Å: Chain B: T.154, I.157, A.158, V.161, A.165, W.179 Chain C: L.73, V.77, A.80, S.81, G.84, L.89, T.90, W.121, L.129, M.133 Ligands: L3P.9 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain C Hydrophobic interactions: B:I.157, B:A.158, B:A.165, B:W.179, C:L.73, C:V.77, C:A.80, C:L.89, C:L.89, C:L.89, C:T.90, C:W.121, C:L.129 L3P.15: 5 residues within 4Å: Chain C: S.92, L.94, W.121, L.164, L.168 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.121, C:W.121, C:L.164, C:L.168

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

BNG.5: 7 residues within 4Å: Chain A: A.98, G.99, H.173, L.174, W.177 Ligands: BNG.6, BNG.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.98, A:H.173 Water bridges: A:H.173 Salt bridges: A:H.173 BNG.6: 5 residues within 4Å: Chain A: G.99, F.101, H.173, W.177 Ligands: BNG.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.101 Hydrogen bonds: A:G.99 Salt bridges: A:H.173 BNG.7: 5 residues within 4Å: Chain A: F.25, E.26, I.42 Chain C: M.175, F.178 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.42, C:F.178 Hydrogen bonds: A:E.26, A:E.26 BNG.11: 7 residues within 4Å: Chain A: L.174, M.175, F.178 Chain B: F.25, E.26, Y.39 Ligands: BNG.5 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.178, A:F.178, B:Y.39 Hydrogen bonds: B:E.26, B:E.26 Water bridges: B:R.22 BNG.12: 11 residues within 4Å: Chain B: T.151, F.155, I.182, A.185, V.189, Y.192, I.193, E.197 Chain C: I.49, V.53, K.65 10 PLIP interactions: 2 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:I.49, B:F.155, B:F.155, B:I.182, B:V.189 Hydrogen bonds: C:K.65, B:E.197 Water bridges: B:T.151, B:E.197, B:E.197 BNG.16: 12 residues within 4Å: Chain A: I.49, V.53, K.65, V.76 Chain C: T.151, F.155, I.182, A.185, V.189, Y.192, I.193, E.197 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:I.49, A:V.76, A:V.76, C:F.155, C:F.155, C:I.182, C:A.185, C:V.189 Hydrogen bonds: A:K.65, A:K.65, C:E.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chan, S.K. et al., Crystal Structure of the 11-cis Isomer of Pharaonis Halorhodopsin: Structural Constraints on Interconversions among Different Isomeric States. Biochemistry (2016)

Release Date

2016-07-27

Peptides

Halorhodopsin: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Membrane

We predict this structure to be a membrane protein.
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Halorhodopsin

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