SMTL ID : 6su3.1

Crystal structure of the 48C12 heliorhodopsin in the violet form at pH 8.8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

26 x LFA: EICOSANE(Non-covalent)(Non-functional Binders)

LFA.1: 4 residues within 4Å: Chain A: R.17, F.81, S.84 Ligands: LFA.11 Ligand excluded by PLIP LFA.5: 14 residues within 4Å: Chain A: F.162, C.166, G.169, I.170, W.173, F.203, F.206, N.207, A.210, L.211, Y.214 Ligands: LFA.6, LFA.16, RET.17 Ligand excluded by PLIP LFA.6: 9 residues within 4Å: Chain A: W.163, C.166, I.167, I.170, F.203, N.207 Ligands: LFA.5, LFA.16, LFA.23 Ligand excluded by PLIP LFA.7: 10 residues within 4Å: Chain A: S.109, F.135, G.136, A.139, W.146 Chain B: L.160, F.164, I.167, V.171 Ligands: LFA.34 Ligand excluded by PLIP LFA.8: 6 residues within 4Å: Chain A: I.60 Chain B: I.174, I.178, P.183 Ligands: LFA.9, LFA.32 Ligand excluded by PLIP LFA.9: 5 residues within 4Å: Chain A: M.41, L.61, E.62, L.132 Ligands: LFA.8 Ligand excluded by PLIP LFA.10: 2 residues within 4Å: Chain A: A.68, V.117 Ligand excluded by PLIP LFA.11: 3 residues within 4Å: Chain A: L.78, F.81 Ligands: LFA.1 Ligand excluded by PLIP LFA.12: 3 residues within 4Å: Chain A: I.18, L.25 Ligands: OLC.3 Ligand excluded by PLIP LFA.13: 5 residues within 4Å: Chain A: F.22, Q.26, W.246 Ligands: LFA.14, LFA.15 Ligand excluded by PLIP LFA.14: 2 residues within 4Å: Chain A: W.246 Ligands: LFA.13 Ligand excluded by PLIP LFA.15: 7 residues within 4Å: Chain A: F.22, Q.26, S.242, W.246, Q.247 Ligands: OLC.2, LFA.13 Ligand excluded by PLIP LFA.16: 2 residues within 4Å: Ligands: LFA.5, LFA.6 Ligand excluded by PLIP LFA.22: 13 residues within 4Å: Chain B: F.162, W.163, C.166, G.169, I.170, W.173, F.203, F.206, N.207, A.210, L.211, Y.214 Ligands: RET.35 Ligand excluded by PLIP LFA.23: 10 residues within 4Å: Chain A: F.164, I.167, V.171 Chain B: S.109, L.132, F.135, A.139 Ligands: LFA.6, LFA.30, LFA.33 Ligand excluded by PLIP LFA.24: 5 residues within 4Å: Chain B: W.246, Q.247, S.250 Ligands: OLA.19, LFA.29 Ligand excluded by PLIP LFA.25: 6 residues within 4Å: Chain B: W.163, C.166, I.167, I.170, N.207 Ligands: OLA.20 Ligand excluded by PLIP LFA.26: 5 residues within 4Å: Chain A: I.178, P.183 Chain B: I.60, L.132 Ligands: LFA.33 Ligand excluded by PLIP LFA.27: 4 residues within 4Å: Chain B: L.67, A.70, L.71, G.74 Ligand excluded by PLIP LFA.28: 3 residues within 4Å: Chain B: Q.26, W.246 Ligands: LFA.29 Ligand excluded by PLIP LFA.29: 6 residues within 4Å: Chain B: F.22, Q.26, S.242, W.246 Ligands: LFA.24, LFA.28 Ligand excluded by PLIP LFA.30: 4 residues within 4Å: Chain B: V.106, L.110, W.146 Ligands: LFA.23 Ligand excluded by PLIP LFA.31: 3 residues within 4Å: Chain B: V.21, F.22, L.25 Ligand excluded by PLIP LFA.32: 3 residues within 4Å: Chain B: L.177, I.178 Ligands: LFA.8 Ligand excluded by PLIP LFA.33: 7 residues within 4Å: Chain B: M.41, I.128, L.131, L.132, F.135 Ligands: LFA.23, LFA.26 Ligand excluded by PLIP LFA.34: 1 residues within 4Å: Ligands: LFA.7 Ligand excluded by PLIP

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

OLC.2: 7 residues within 4Å: Chain A: P.192, G.193, F.194, S.201, V.239, Q.247 Ligands: LFA.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.239 Hydrogen bonds: A:G.193 Water bridges: A:F.194 OLC.3: 4 residues within 4Å: Chain A: N.14, R.17, I.18 Ligands: LFA.12 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.17 OLC.21: 6 residues within 4Å: Chain B: G.193, G.197, I.200, L.204, F.205 Ligands: OLA.19 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.200, B:L.204, B:F.205

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

SO4.4: 3 residues within 4Å: Chain A: K.98, Q.100, K.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.100 Water bridges: A:K.150, A:K.150 Salt bridges: A:K.98, A:K.150

2 x RET: RETINAL(Covalent)

RET.17: 18 residues within 4Å: Chain A: W.105, Y.108, S.111, S.112, M.115, M.141, I.142, G.145, F.162, G.165, C.166, F.206, F.209, A.210, Q.213, S.237, K.241 Ligands: LFA.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.108, A:I.142, A:F.162, A:F.206, A:F.206, A:F.209, A:F.209, A:F.209, A:F.209, A:F.209, A:F.209, A:A.210, A:K.241 RET.35: 18 residues within 4Å: Chain B: W.105, Y.108, S.111, S.112, M.115, M.141, I.142, G.145, F.162, G.165, C.166, F.206, F.209, A.210, Q.213, S.237, K.241 Ligands: LFA.22 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.105, B:W.105, B:Y.108, B:Y.108, B:F.162, B:F.206, B:F.206, B:F.209, B:F.209, B:F.209, B:F.209, B:F.209, B:A.210, B:K.241

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 3 residues within 4Å: Chain B: P.192, G.193 Ligands: OLA.19 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.193 Water bridges: B:F.194

2 x OLA: OLEIC ACID(Non-covalent)

OLA.19: 7 residues within 4Å: Chain B: G.193, F.194, F.205, Q.247 Ligands: GOL.18, OLC.21, LFA.24 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.205 Water bridges: B:F.194 OLA.20: 8 residues within 4Å: Chain B: I.170, W.173, I.174, V.180, Y.196, I.199, F.203 Ligands: LFA.25 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.170, B:W.173, B:I.174, B:Y.196, B:I.199, B:F.203, B:F.203, B:F.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalev, K. et al., High-resolution structural insights into the heliorhodopsin family. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2019-12-11

Peptides

48C12 heliorhodopsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
A

Membrane

We predict this structure to be a membrane protein.
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48C12 heliorhodopsin

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