SMTL ID : 6djt.1

Structure of TYW1 with a lysine-pyruvate adduct bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

monomer

Ligands

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 5 residues within 4Å: Chain A: C.46, C.59, K.61, T.69, C.72 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.46, A:C.59, A:C.72

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: L.120, K.124, L.146, P.148 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.124 GOL.3: 4 residues within 4Å: Chain A: R.246, D.250, E.292, K.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.292, A:K.295 Water bridges: A:R.246 GOL.4: 5 residues within 4Å: Chain A: K.63, D.311, S.312, E.313, D.314 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.63, A:D.311, A:E.313, A:D.314, A:D.314 Water bridges: A:K.63, A:S.312, A:S.312 GOL.5: 7 residues within 4Å: Chain A: I.153, S.154, G.157, P.159, V.182, R.241 Ligands: FS0.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.182, A:R.241, A:R.241 Water bridges: A:S.154, A:S.154 GOL.6: 6 residues within 4Å: Chain A: A.131, G.132, V.133, L.134, D.135, R.136 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.133, A:L.134, A:D.135, A:R.136 GOL.7: 9 residues within 4Å: Chain A: Y.206, R.213, G.247, Y.248, N.249, D.250, D.251, K.254 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.206, A:N.249, A:D.251, A:D.251 GOL.8: 7 residues within 4Å: Chain A: Y.206, D.207, D.209, S.210, R.213, K.254 Ligands: GOL.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.209, A:D.209, A:R.213, A:R.213, A:K.254, A:K.254 GOL.9: 6 residues within 4Å: Chain A: R.246, K.284, E.285, M.287, Q.289, R.316 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.246, A:E.285, A:R.316, A:R.316

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

PEG.10: 3 residues within 4Å: Chain A: Q.321, I.327, N.328 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.321 Water bridges: A:I.309 PEG.11: 4 residues within 4Å: Chain A: E.192, E.195, E.234, K.235 No protein-ligand interaction detected (PLIP)

1 x FS0: FE2/S3 CLUSTER(Non-covalent)

FS0.12: 7 residues within 4Å: Chain A: C.82, Q.84, N.85, C.86, C.89, G.157 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.82, A:C.86, A:C.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grell, T.A.J. et al., Biochemical and Structural Characterization of a Schiff Base in the Radical-Mediated Biosynthesis of 4-Demethylwyosine by TYW1. J. Am. Chem. Soc. (2018)

Release Date

2018-06-13

Peptides

S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase