SMTL ID : 8vcw.1

X-Ray Crystal Structure of the biotin synthase from B. obeum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.1: 20 residues within 4Å: Chain A: Y.68, V.108, T.109, G.111, S.140, G.142, H.161, N.163, E.165, K.183, I.202, N.230, A.231, L.232, M.233, I.235, A.271, L.297 Ligands: SF4.4, DTB.5 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:G.111, A:G.111, A:G.142, A:N.163, A:E.165, A:M.233, A:M.233 Water bridges: A:S.140, A:H.161, A:H.162, A:K.183, A:K.183, A:K.183, A:K.183, A:K.183, A:I.235 Salt bridges: A:K.183 pi-Stacking: A:Y.68

1 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.2: 2 residues within 4Å: Chain A: H.74 Ligands: FE.6 No protein-ligand interaction detected (PLIP)

1 x Q46: Fe4 H S5(Non-covalent)

Q46.3: 11 residues within 4Å: Chain A: C.52, S.53, R.104, S.106, V.108, C.138, S.140, H.161, C.198, R.268 Ligands: DTB.5 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.52, A:C.138, A:C.198

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

SF4.4: 10 residues within 4Å: Chain A: C.62, E.64, C.66, Y.68, C.69, S.72, A.110, G.111, H.178 Ligands: SAM.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Salt bridges: A:E.165 Metal complexes: A:C.62, A:C.66, A:C.69, SAM.1

1 x DTB: 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID(Non-covalent)

DTB.5: 13 residues within 4Å: Chain A: I.54, H.161, N.163, P.228, N.230, A.271, I.292, M.296, L.297, T.298, T.299 Ligands: SAM.1, Q46.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.297 Hydrogen bonds: A:H.161, A:N.163, A:N.230, A:N.230, A:L.297, A:T.298, A:T.299, A:T.299

1 x FE: FE (III) ION(Non-covalent)

FE.6: 2 residues within 4Å: Chain A: H.74 Ligands: BTB.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.74

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

CL.7: 4 residues within 4Å: Chain A: F.171, P.172, T.179, Y.180 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lachowicz, J.C. et al., Discovery of a Biotin Synthase That Utilizes an Auxiliary 4Fe-5S Cluster for Sulfur Insertion. J.Am.Chem.Soc. (2024)

Release Date

2024-01-24

Peptides

Biotin synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Biotin synthase