SMTL ID : 6s63.1

Dark-adapted structure of Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich at room temperature

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 20 residues within 4Å: Chain A: Y.87, W.90, T.93, T.94, L.97, M.122, I.123, G.126, W.142, S.145, T.146, M.149, W.186, Y.189, P.190, W.193, F.212, D.216, A.219, K.220 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.94, A:L.97, A:M.149, A:W.186, A:Y.189, A:Y.189, A:Y.189, A:Y.189, A:P.190, A:W.193, A:K.220

4 x R16: HEXADECANE(Non-covalent)

R16.2: 11 residues within 4Å: Chain A: Y.4, L.15, W.16, I.19, L.23, L.210, M.213, V.214, V.217 Ligands: R16.4, DD9.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.23 R16.3: 9 residues within 4Å: Chain A: I.150, L.153, Y.154, A.157, L.183, V.184, T.187, A.188, I.191 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.187 R16.4: 10 residues within 4Å: Chain A: L.23, I.26, G.27, Y.30, V.217, T.218, V.221, G.222, F.225 Ligands: R16.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.30, A:Y.30, A:V.217, A:F.225 R16.5: 11 residues within 4Å: Chain A: D.108, V.110, T.111, T.114, V.118, L.121, F.144, I.147, C.148, V.151, F.155 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.118

5 x DD9: nonane(Non-covalent)

DD9.6: 5 residues within 4Å: Chain A: I.136, A.137, S.140, W.141, F.144 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.141, A:W.141, A:F.144 DD9.7: 9 residues within 4Å: Chain A: L.6, L.15, G.18, I.19, T.21, L.22, L.62, F.65 Ligands: DD9.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.6, A:T.21, A:L.22, A:L.62 DD9.8: 6 residues within 4Å: Chain A: A.59, L.62, S.63, F.66, I.68 Ligands: DD9.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.59, A:L.62 DD9.9: 6 residues within 4Å: Chain A: Y.4, L.6, L.15, I.19 Ligands: R16.2, DD9.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.4, A:L.15 DD9.10: 8 residues within 4Å: Chain A: T.28, L.32, I.51, L.52, G.55, I.56, A.59 Ligands: DD9.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.52

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 3 residues within 4Å: Chain A: D.40, D.42, L.234 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.40, A:D.42, A:L.234, H2O.2, H2O.2

1 x NA: SODIUM ION(Non-functional Binders)

NA.12: 7 residues within 4Å: Chain A: D.5, L.6, L.7, G.8, D.9, R.11, T.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.7, A:G.8, A:D.9, A:D.9, A:R.11

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

CL.13: 6 residues within 4Å: Chain A: Q.1, A.2, G.204, L.205, G.206, I.207 Ligand excluded by PLIP CL.14: 2 residues within 4Å: Chain A: D.40, K.41 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: V.38, T.39, D.40, L.234 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Axford, D. et al., Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts. Acta Crystallogr D Struct Biol (2022)

Release Date

2020-07-22

Peptides

Archaerhodopsin-3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Archaerhodopsin-3

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