SMTL ID : 6guy.1

Room temperature structure of Archaerhodopsin-3 via LCP extruder using synchrotron radiation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: W.90, T.93, T.94, L.97, M.122, G.126, W.142, S.145, T.146, M.149, W.186, Y.189, P.190, W.193, D.216, A.219, K.220 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.90, A:W.90, 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:Y.189, A:P.190, A:W.193, A:W.193, A:A.219, A:K.220

5 x R16: HEXADECANE(Non-covalent)

R16.2: 3 residues within 4Å: Chain A: I.19, V.214 Ligands: DD9.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.19, A:V.214 R16.3: 4 residues within 4Å: Chain A: A.157, L.183, V.184, T.187 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.157, A:V.184 R16.4: 5 residues within 4Å: Chain A: L.23, I.26, Y.30, V.217, V.221 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.23, A:I.26, A:Y.30, A:Y.30, A:V.217, A:V.221 R16.5: 7 residues within 4Å: Chain A: D.108, V.110, T.111, T.114, V.118, L.121, C.148 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.114, A:V.118, A:L.121 R16.11: 3 residues within 4Å: Chain A: S.140, F.144 Ligands: DD9.6 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.144, A:F.144

5 x DD9: nonane(Non-covalent)

DD9.6: 4 residues within 4Å: Chain A: A.137, S.140, W.141 Ligands: R16.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.137, A:W.141 DD9.7: 4 residues within 4Å: Chain A: L.6, G.18, L.22, L.62 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.6, A:L.22, A:L.22, A:L.62 DD9.8: 4 residues within 4Å: Chain A: A.59, L.62, F.66, I.68 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.59, A:L.62, A:I.68 DD9.9: 2 residues within 4Å: Chain A: L.15 Ligands: R16.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.15 DD9.10: 3 residues within 4Å: Chain A: I.51, L.52, G.55 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.51, A:L.52

1 x CA: CALCIUM ION(Non-covalent)

CA.12: 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.1, H2O.1

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

NA.13: 7 residues within 4Å: Chain A: D.5, L.6, L.7, G.8, D.9, R.11, T.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.6, A:L.7, A:G.8, A:D.9

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

CL.14: 6 residues within 4Å: Chain A: Q.1, A.2, G.204, L.205, G.206, I.207 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain A: D.40, K.41 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: V.38, T.39, D.40 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bada Juarez, J.F. et al., Room temperature structure of Archaerhodopsin-3 via LCP extruder using synchrotron radiation. To Be Published

Release Date

2019-10-09

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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