SMTL ID : 7omo.1 (1 other biounit)

Crystal structure of coelenteramine-bound Renilla reniformis luciferase RLuc8-D120A variant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x VKB: 4-[5-azanyl-6-(phenylmethyl)pyrazin-2-yl]phenol(Non-covalent)

VKB.1: 12 residues within 4Å: Chain A: W.121, I.150, W.156, D.162, I.166, F.180, F.181, P.220, I.223, F.261, F.262 Ligands: CL.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.150, A:W.156, A:W.156, A:D.162, A:I.166, A:P.220, A:I.223, A:I.223, A:F.262 pi-Stacking: A:W.156, A:F.180, A:F.181

2 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.2: 1 residues within 4Å: Chain A: E.9 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.9 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.4: 5 residues within 4Å: Chain A: N.53, W.121, W.219, P.220 Ligands: VKB.1 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: D.31, S.32, F.33, G.85, K.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.32, A:K.86 Water bridges: A:S.32 GOL.6: 5 residues within 4Å: Chain A: A.43, E.44, N.109, L.110, P.111 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.44, A:L.110 GOL.7: 2 residues within 4Å: Chain A: D.31, G.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schenkmayerova, A. et al., Catalytic mechanism for Renilla-type luciferases. Nat Catal (2023)

Release Date

2022-06-01

Peptides

Renilla reniformis luciferase RLuc8-D120A variant: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Renilla reniformis luciferase RLuc8-D120A variant

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