SMTL ID : 7clj.1

Crystal structure of Thermoplasmatales archaeon heliorhodopsin E108D mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 17 residues within 4Å: Chain A: W.112, Y.115, S.118, A.119, M.122, M.148, N.149, G.152, Y.170, G.173, C.174, F.209, F.212, A.213, M.216, K.244 Ligands: OLC.10 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.112, A:W.112, A:Y.115, A:Y.115, A:A.119, A:Y.170, A:Y.170, A:F.209, A:F.209, A:F.212, A:F.212, A:F.212, A:F.212, A:F.212, A:A.213, A:K.244 RET.18: 17 residues within 4Å: Chain B: W.112, Y.115, S.118, A.119, M.122, M.148, N.149, G.152, Y.170, G.173, C.174, F.209, F.212, A.213, M.216, K.244 Ligands: OLC.27 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.112, B:W.112, B:Y.115, B:Y.115, B:A.119, B:Y.170, B:Y.170, B:F.209, B:F.209, B:F.212, B:F.212, B:F.212, B:F.212, B:F.212, B:A.213, B:K.244

30 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)(Non-functional Binders)

OLC.2: 5 residues within 4Å: Chain A: F.197, Y.200, Q.250 Ligands: OLC.3, OLC.5 Ligand excluded by PLIP OLC.3: 9 residues within 4Å: Chain A: I.28, Q.32, S.245, A.246, W.249, Q.250, A.253 Ligands: OLC.2, OLC.5 Ligand excluded by PLIP OLC.5: 2 residues within 4Å: Ligands: OLC.2, OLC.3 Ligand excluded by PLIP OLC.6: 4 residues within 4Å: Chain A: I.117, L.138, L.139, F.142 Ligand excluded by PLIP OLC.7: 4 residues within 4Å: Chain A: Y.54, N.55, E.56, I.57 Ligand excluded by PLIP OLC.8: 1 residues within 4Å: Chain A: Y.38 Ligand excluded by PLIP OLC.9: 1 residues within 4Å: Chain A: T.93 Ligand excluded by PLIP OLC.10: 8 residues within 4Å: Chain A: Y.170, C.174, F.178, W.181, N.210, A.213, I.214 Ligands: RET.1 Ligand excluded by PLIP OLC.11: 4 residues within 4Å: Chain A: K.17, I.20, I.24 Ligands: OLC.14 Ligand excluded by PLIP OLC.12: 7 residues within 4Å: Chain A: F.113, S.116, F.142, L.150 Chain B: T.168, I.175 Ligands: OLC.30 Ligand excluded by PLIP OLC.13: 6 residues within 4Å: Chain A: T.165, N.166, W.167, T.168, I.171 Ligands: OLC.29 Ligand excluded by PLIP OLC.14: 5 residues within 4Å: Chain A: K.17, F.18, F.21, K.234 Ligands: OLC.11 Ligand excluded by PLIP OLC.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OLC.16: 3 residues within 4Å: Chain A: R.19, V.27, A.92 Ligand excluded by PLIP OLC.17: 1 residues within 4Å: Chain A: R.98 Ligand excluded by PLIP OLC.19: 5 residues within 4Å: Chain B: F.197, Y.200, Q.250 Ligands: OLC.20, OLC.22 Ligand excluded by PLIP OLC.20: 9 residues within 4Å: Chain B: I.28, Q.32, S.245, A.246, W.249, Q.250, A.253 Ligands: OLC.19, OLC.22 Ligand excluded by PLIP OLC.22: 2 residues within 4Å: Ligands: OLC.19, OLC.20 Ligand excluded by PLIP OLC.23: 4 residues within 4Å: Chain B: I.117, L.138, L.139, F.142 Ligand excluded by PLIP OLC.24: 4 residues within 4Å: Chain B: Y.54, N.55, E.56, I.57 Ligand excluded by PLIP OLC.25: 1 residues within 4Å: Chain B: Y.38 Ligand excluded by PLIP OLC.26: 1 residues within 4Å: Chain B: T.93 Ligand excluded by PLIP OLC.27: 8 residues within 4Å: Chain B: Y.170, C.174, F.178, W.181, N.210, A.213, I.214 Ligands: RET.18 Ligand excluded by PLIP OLC.28: 4 residues within 4Å: Chain B: K.17, I.20, I.24 Ligands: OLC.31 Ligand excluded by PLIP OLC.29: 7 residues within 4Å: Chain A: T.168, I.175 Chain B: F.113, S.116, F.142, L.150 Ligands: OLC.13 Ligand excluded by PLIP OLC.30: 6 residues within 4Å: Chain B: T.165, N.166, W.167, T.168, I.171 Ligands: OLC.12 Ligand excluded by PLIP OLC.31: 5 residues within 4Å: Chain B: K.17, F.18, F.21, K.234 Ligands: OLC.28 Ligand excluded by PLIP OLC.32: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP OLC.33: 3 residues within 4Å: Chain B: R.19, V.27, A.92 Ligand excluded by PLIP OLC.34: 1 residues within 4Å: Chain B: R.98 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 7 residues within 4Å: Chain A: C.211, I.214, N.215, L.218, W.226, V.235, L.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.215 SO4.21: 7 residues within 4Å: Chain B: C.211, I.214, N.215, L.218, W.226, V.235, L.239 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, T. et al., Structural basis for unique color tuning mechanism in heliorhodopsin. Biochem.Biophys.Res.Commun. (2020)

Release Date

2020-09-02

Peptides

heliorhodopsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Membrane

We predict this structure to be a membrane protein.
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heliorhodopsin