SMTL ID : 3abw.1

Crystal structure of pharaonis halorhodopsin in complex with azide ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: 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, 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:W.222, A:Y.225, 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.7: 15 residues within 4Å: Chain B: 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 16 PLIP interactions: 16 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: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:K.256 RET.13: 15 residues within 4Å: Chain C: 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 C Hydrophobic interactions: C:W.127, C:W.127, C:T.131, C:Y.180, 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:K.256

2 x 22B: BACTERIORUBERIN(Non-covalent)

22B.2: 14 residues within 4Å: Chain A: G.46, I.49, V.53, T.56, K.65, V.69, I.72 Chain C: K.148, T.151, F.155, A.185, V.189, I.193, E.197 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain C Hydrophobic interactions: A:I.49, A:V.69, A:I.72, C:T.151, C:F.155, C:F.155, C:A.185, C:V.189, C:I.193 Hydrogen bonds: A:K.65, A:K.65, C:K.148 22B.11: 14 residues within 4Å: Chain A: T.147, T.151, F.155, A.185, V.189, I.193, E.197 Chain B: G.46, I.49, V.53, T.56, V.69, I.72, I.79 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:T.147, A:T.151, A:F.155, A:F.155, A:A.185, A:I.193, B:I.49, B:V.53, B:V.69, B:I.72, B:I.79

9 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: F.150, I.153, T.154, I.157, A.158, V.161 Chain B: V.77, L.129 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.77, B:L.129, B:L.129, A:F.150, A:I.153, A:I.157, A:I.157, A:V.161 L3P.4: 10 residues within 4Å: Chain A: S.92, V.93, L.94, W.121, L.125, L.164, L.168 Ligands: L3P.5, L3P.8, L3P.9 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.94, A:W.121, A:W.121, A:L.125, A:L.164, A:L.168, A:L.168 L3P.5: 12 residues within 4Å: Chain A: Q.21, A.80, L.89, T.90, W.121, L.125, T.126 Chain C: V.161, T.162, W.179 Ligands: L3P.4, L3P.16 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:L.89, A:T.90, A:W.121, A:L.125, A:T.126, C:V.161, C:T.162, C:W.179, C:W.179 L3P.8: 13 residues within 4Å: Chain A: V.161, L.168, W.179 Chain B: V.19, Q.21, A.80, S.81, L.89, T.90, W.121, T.126 Ligands: L3P.4, L3P.9 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Q.21, B:A.80, B:L.89, B:L.89, B:L.89, B:T.90, B:W.121, B:T.126, A:V.161, A:L.168, A:W.179 L3P.9: 9 residues within 4Å: Chain B: S.92, V.93, L.94, W.121, L.164, L.168 Ligands: L3P.4, L3P.8, L3P.15 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.121, B:W.121, B:L.164, B:L.168 L3P.10: 8 residues within 4Å: Chain B: A.146, L.149, F.150, I.153, I.157, A.158 Chain C: V.77, M.133 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:V.77, B:I.153, B:I.157, B:I.157 L3P.14: 6 residues within 4Å: Chain A: L.129 Chain C: L.149, F.150, I.153, T.154, I.157 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.149, C:I.153, C:I.153, C:I.157, A:L.129 L3P.15: 11 residues within 4Å: Chain B: V.161, L.164, L.168 Chain C: V.19, Q.21, A.80, L.89, W.121, T.126 Ligands: L3P.9, L3P.16 9 PLIP interactions: 7 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Q.21, C:A.80, C:L.89, C:L.89, C:W.121, C:W.121, C:T.126, B:V.161, B:L.164 L3P.16: 5 residues within 4Å: Chain C: W.121, L.125, L.164 Ligands: L3P.5, L3P.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.121, C:W.121, C:L.164

3 x AZI: AZIDE ION(Non-covalent)

AZI.6: 9 residues within 4Å: Chain A: V.77, S.78, S.81, Y.82, T.126, W.127, S.130, D.252, K.256 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.78, A:S.81, A:T.126, A:S.130, A:S.130 AZI.12: 8 residues within 4Å: Chain B: V.77, S.78, S.81, T.126, W.127, S.130, D.252, K.256 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.78, B:S.81, B:T.126, B:S.130, B:S.130 AZI.17: 6 residues within 4Å: Chain C: S.78, S.81, T.126, W.127, S.130, K.256 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.78, C:S.81, C:T.126, C:T.126, C:S.130, C:K.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanada, S. et al., Binding mode of azide ion to pharaonis halorhodopsin. To be Published

Release Date

2011-02-02

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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