SMTL ID : 6s6c.1

Ground state structure of Archaerhodopsin-3 at 100K

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.07 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.90, A:T.94, A:M.149, A:Y.189, A:Y.189, A:Y.189, A:P.190, A:W.193, A:A.219, A:K.220

6 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, DD9.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.15, A:W.16, A:I.19, A:L.23, A:V.214 R16.3: 11 residues within 4Å: Chain A: M.149, I.150, L.153, Y.154, A.157, T.158, R.161, L.183, V.184, T.187, 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.30, A:Y.30, A:Y.30, A:V.217, A:T.218 R16.5: 12 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 Ligands: D12.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.151 R16.7: 7 residues within 4Å: Chain A: T.134, I.136, A.137, S.140, W.141, F.144 Ligands: R16.12 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.137, A:W.141, A:W.141, A:F.144 R16.12: 6 residues within 4Å: Chain A: I.136, S.140, L.143, F.144, I.147 Ligands: R16.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.143

1 x D12: DODECANE(Non-covalent)

D12.6: 5 residues within 4Å: Chain A: I.150, V.151, Y.154, F.155 Ligands: R16.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.150, A:Y.154, A:Y.154, A:Y.154, A:F.155, A:F.155

4 x DD9: nonane(Non-covalent)

DD9.8: 10 residues within 4Å: Chain A: L.6, L.15, G.18, I.19, T.21, L.22, L.62, F.65, F.66 Ligands: DD9.10 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.19, A:T.21, A:L.22, A:L.62, A:F.65 DD9.9: 6 residues within 4Å: Chain A: A.59, L.62, S.63, F.66, I.68 Ligands: DD9.11 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.59, A:L.62, A:F.66, A:F.66, A:I.68 DD9.10: 6 residues within 4Å: Chain A: Y.4, L.6, L.15, I.19 Ligands: R16.2, DD9.8 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.4 DD9.11: 8 residues within 4Å: Chain A: T.28, L.32, I.51, L.52, G.55, I.56, A.59 Ligands: DD9.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.51, A:L.52, A:A.59

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 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.3, H2O.3

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

NA.14: 7 residues within 4Å: Chain A: D.5, L.6, L.7, G.8, D.9, R.11, T.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.7, A:G.8, A:T.14

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

CL.15: 6 residues within 4Å: Chain A: Q.1, A.2, G.204, L.205, G.206, I.207 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: D.40, K.41 Ligand excluded by PLIP CL.17: 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

Bada Juarez, J.F. et al., Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization. Nat Commun (2021)

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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