SMTL ID : 6uh3.1

Crystal structure of bacterial heliorhodopsin 48C12

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x RET: RETINAL(Covalent)

RET.1: 16 residues within 4Å: Chain A: W.103, Y.106, S.109, S.110, M.113, M.139, I.140, G.143, F.160, F.204, F.207, A.208, Q.211, Y.231, S.235, K.239 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.103, A:W.103, A:F.160, A:F.204, A:F.207, A:F.207, A:F.207, A:A.208, A:Q.211, A:K.239 RET.15: 14 residues within 4Å: Chain B: Y.106, S.110, M.113, M.139, I.140, G.143, F.160, G.163, C.164, F.204, F.207, A.208, Q.211, K.239 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.106, B:I.140, B:F.204, B:F.204, B:F.207, B:F.207, B:F.207, B:F.207, B:A.208, B:Q.211, B:K.239

21 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 4 residues within 4Å: Chain A: L.157, W.161, F.162, I.165 Ligand excluded by PLIP PGE.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PGE.4: 2 residues within 4Å: Chain A: F.201 Ligands: PGE.6 Ligand excluded by PLIP PGE.5: 3 residues within 4Å: Chain A: D.34, L.65 Ligands: PGE.9 Ligand excluded by PLIP PGE.6: 1 residues within 4Å: Ligands: PGE.4 Ligand excluded by PLIP PGE.7: 1 residues within 4Å: Chain A: L.209 Ligand excluded by PLIP PGE.8: 3 residues within 4Å: Chain A: S.107, F.133 Ligands: PLM.14 Ligand excluded by PLIP PGE.9: 2 residues within 4Å: Chain A: E.60 Ligands: PGE.5 Ligand excluded by PLIP PGE.10: 2 residues within 4Å: Chain A: L.76, F.79 Ligand excluded by PLIP PGE.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PGE.12: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PGE.16: 2 residues within 4Å: Chain B: Y.194, I.198 Ligand excluded by PLIP PGE.17: 1 residues within 4Å: Ligands: PEG.21 Ligand excluded by PLIP PGE.19: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PGE.20: 2 residues within 4Å: Chain B: L.209, W.221 Ligand excluded by PLIP PGE.22: 3 residues within 4Å: Chain A: I.176 Chain B: I.58, I.126 Ligand excluded by PLIP PGE.23: 2 residues within 4Å: Chain B: F.79, I.80 Ligand excluded by PLIP PGE.24: 2 residues within 4Å: Chain B: S.9, R.229 Ligand excluded by PLIP PGE.25: 5 residues within 4Å: Chain B: C.164, G.167, I.168, N.205, Y.212 Ligand excluded by PLIP PGE.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PGE.27: 1 residues within 4Å: Chain B: S.185 Ligand excluded by PLIP

4 x PLM: PALMITIC ACID(Non-covalent)(Non-functional Binders)

PLM.13: 3 residues within 4Å: Chain A: W.221, R.229, A.230 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.230 Salt bridges: A:R.229 PLM.14: 5 residues within 4Å: Chain A: F.77, R.89, F.101, V.104 Ligands: PGE.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.77, A:F.77, A:F.101, A:V.104 Salt bridges: A:R.89 PLM.28: 5 residues within 4Å: Chain B: K.8, N.12, R.15, I.16, F.20 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.16, B:F.20, B:F.20 Hydrogen bonds: B:N.12 Salt bridges: B:K.8 PLM.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.18: 1 residues within 4Å: Chain B: D.154 No protein-ligand interaction detected (PLIP) PEG.21: 3 residues within 4Å: Chain B: K.216, K.218 Ligands: PGE.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.216, B:K.216

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, Y. et al., Crystal structure of heliorhodopsin 48C12. Cell Res. (2020)

Release Date

2019-12-04

Peptides

Heliorhodopsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Heliorhodopsin