SMTL ID : 6xl3.1 (1 other biounit)

Mastigocladopsis repens rhodopsin chloride pump

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

homo-trimer

Ligands

3 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: F.72, W.75, T.79, L.82, M.107, Y.126, S.129, C.130, Y.133, W.170, Y.173, P.174, W.177, D.200, S.203, K.204 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.72, A:T.79, A:Y.126, A:Y.133, A:W.170, A:W.170, A:Y.173, A:Y.173, A:Y.173, A:Y.173, A:Y.173, A:P.174, A:W.177, A:K.204 RET.7: 16 residues within 4Å: Chain B: F.72, W.75, T.79, L.82, M.107, Y.126, S.129, C.130, Y.133, W.170, Y.173, P.174, W.177, D.200, S.203, K.204 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.72, B:T.79, B:Y.126, B:Y.133, B:W.170, B:W.170, B:Y.173, B:Y.173, B:Y.173, B:Y.173, B:Y.173, B:P.174, B:W.177, B:K.204 RET.13: 16 residues within 4Å: Chain C: F.72, W.75, T.79, L.82, M.107, Y.126, S.129, C.130, Y.133, W.170, Y.173, P.174, W.177, D.200, S.203, K.204 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:F.72, C:T.79, C:Y.126, C:Y.133, C:W.170, C:W.170, C:Y.173, C:Y.173, C:Y.173, C:Y.173, C:Y.173, C:P.174, C:W.177, C:K.204

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 7 residues within 4Å: Chain A: I.45, A.46, L.49, T.74, W.75, S.78, K.204 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: N.60, V.61 Ligand excluded by PLIP CL.8: 7 residues within 4Å: Chain B: I.45, A.46, L.49, T.74, W.75, S.78, K.204 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain B: N.60, V.61 Ligand excluded by PLIP CL.14: 7 residues within 4Å: Chain C: I.45, A.46, L.49, T.74, W.75, S.78, K.204 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain C: N.60, V.61 Ligand excluded by PLIP

6 x C14: TETRADECANE(Non-covalent)

C14.4: 10 residues within 4Å: Chain A: I.34, T.37, L.38, F.41, I.45, L.81 Chain C: L.94, G.98, G.102 Ligands: C14.5 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.34, A:T.37, A:L.38, A:F.41, A:F.41, A:I.45, A:L.81, C:L.94 C14.5: 10 residues within 4Å: Chain A: G.48, A.52, L.57, G.58, V.70, T.74 Chain C: Y.106, V.109, V.113 Ligands: C14.4 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:A.52, A:L.57, A:V.70, A:T.74, C:Y.106, C:Y.106, C:V.109, C:V.113 C14.10: 10 residues within 4Å: Chain A: L.94, G.98, G.102 Chain B: I.34, T.37, L.38, F.41, I.45, L.81 Ligands: C14.11 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.34, B:T.37, B:L.38, B:F.41, B:F.41, B:I.45, B:L.81, A:L.94 C14.11: 10 residues within 4Å: Chain A: Y.106, V.109, V.113 Chain B: G.48, A.52, L.57, G.58, V.70, T.74 Ligands: C14.10 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.106, A:Y.106, A:V.109, A:V.113, B:A.52, B:L.57, B:V.70, B:T.74 C14.16: 10 residues within 4Å: Chain B: L.94, G.98, G.102 Chain C: I.34, T.37, L.38, F.41, I.45, L.81 Ligands: C14.17 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.34, C:T.37, C:L.38, C:F.41, C:F.41, C:I.45, C:L.81, B:L.94 C14.17: 10 residues within 4Å: Chain B: Y.106, V.109, V.113 Chain C: G.48, A.52, L.57, G.58, V.70, T.74 Ligands: C14.16 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:A.52, C:L.57, C:V.70, C:T.74, B:Y.106, B:Y.106, B:V.109, B:V.113

3 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.6: 6 residues within 4Å: Chain A: T.87, F.88, R.91, T.92, L.94, T.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.87, A:T.87 BOG.12: 6 residues within 4Å: Chain B: T.87, F.88, R.91, T.92, L.94, T.97 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.87, B:T.87 BOG.18: 6 residues within 4Å: Chain C: T.87, F.88, R.91, T.92, L.94, T.97 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.87, C:T.87

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Besaw, J.E. et al., The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants. J.Biol.Chem. (2020)

Release Date

2020-07-29

Peptides

Mastigocladopsis repens rhodopsin chloride pump: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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Mastigocladopsis repens rhodopsin chloride pump

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