SMTL ID : 7zy3.1

Room temperature structure of Archaerhodopsin-3 obtained 110 ns after photoexcitation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.90, A:T.94, A:L.97, A:M.149, A:W.186, A:W.186, A:Y.189, A:Y.189, A:Y.189, A:Y.189, A:Y.189, A:P.190, A:P.190, A:W.193, A:K.220, A:K.220

1 x DD9: nonane(Non-covalent)

DD9.2: 6 residues within 4Å: Chain A: T.134, I.136, A.137, S.140, W.141, F.144 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.136

1 x R16: HEXADECANE(Non-covalent)

R16.3: 10 residues within 4Å: Chain A: Y.4, L.15, W.16, I.19, L.23, L.210, M.213, V.214, V.217 Ligands: PLM.5 No protein-ligand interaction detected (PLIP)

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.4: 10 residues within 4Å: Chain A: I.150, L.153, Y.154, A.157, T.158, L.183, V.184, T.187, A.188, I.191 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.157, A:T.187 PLM.5: 10 residues within 4Å: Chain A: L.23, T.177, V.217, T.218, V.221, G.222, F.225, I.226, R.229 Ligands: R16.3 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.217, A:I.226 Water bridges: A:R.229 Salt bridges: A:R.229

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 3 residues within 4Å: Chain A: D.40, D.42, L.234 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.40, A:D.40, A:D.42, A:L.234, H2O.2

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

NA.7: 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:R.11, A:T.14

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain A: D.236, T.237, E.238 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.236, A:T.237, H2O.1, H2O.1, H2O.2

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

CL.9: 2 residues within 4Å: Chain A: D.40, K.41 Ligand excluded by PLIP CL.10: 6 residues within 4Å: Chain A: Q.1, A.2, G.204, L.205, G.206, I.207 Ligand excluded by PLIP CL.11: 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

Birch, J. et al., A versatile approach to high-density microcrystals in lipidic cubic phase for room-temperature serial crystallography. J.Appl.Crystallogr. (2023)

Release Date

2023-06-14

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