SMTL ID : 9aub.1

PLP-dependent BesB-F231Y variant holoenzyme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 6 residues within 4Å: Chain A: D.21, G.22, R.24, I.26, P.33, F.469 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.24, A:P.33 Water bridges: A:L.23 EDO.2: 5 residues within 4Å: Chain A: A.204, R.206, L.366, P.367, E.372 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.206, A:R.206, A:E.372 Water bridges: A:L.205 EDO.5: 1 residues within 4Å: Chain A: G.126 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.166

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: T.99, R.100, S.101, V.128, L.129, S.130, L.155, Q.159 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.100, A:A.102, A:S.130, A:S.130, A:Q.159 Water bridges: A:S.130, A:S.130 GOL.4: 3 residues within 4Å: Chain A: E.53, F.70, V.478 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.478 Water bridges: A:Y.52, A:Y.52

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 1 residues within 4Å: Chain A: R.423 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hedges, J.B. et al., Terminal alkyne formation by a pyridoxal phosphate-dependent enzyme. Nat.Chem.Biol. (2025)

Release Date

2025-07-02

Peptides

BesB F231Y variant: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BesB F231Y variant