SMTL ID : 1r30.1

The Crystal Structure of Biotin Synthase, an S-Adenosylmethionine-Dependent Radical Enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.40 Å

Oligo State

homo-dimer

Ligands

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

SAM.1: 17 residues within 4Å: Chain A: Y.82, P.84, A.123, W.125, T.153, G.155, N.174, N.176, D.178, R.196, I.215, M.246, L.247, V.248, L.314 Ligands: SF4.2, DTB.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.82, A:W.125, A:W.125, A:N.176, A:D.178, A:V.248, A:V.248 Salt bridges: A:H.175, A:R.191, A:R.196 SAM.6: 18 residues within 4Å: Chain B: Y.82, P.84, A.123, W.125, T.153, G.155, N.174, H.175, N.176, D.178, R.196, I.215, M.246, L.247, V.248, L.314 Ligands: SF4.7, DTB.9 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.82, B:W.125, B:T.153, B:N.176, B:D.178, B:V.248, B:V.248 Salt bridges: B:H.175, B:R.191, B:R.196

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

SF4.2: 7 residues within 4Å: Chain A: C.76, E.78, C.80, C.83, S.86, A.124 Ligands: SAM.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.76, A:C.80, A:C.83, SAM.1 SF4.7: 7 residues within 4Å: Chain B: C.76, E.78, C.80, C.83, S.86, A.124 Ligands: SAM.6 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.76, B:C.80, B:C.83

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.3: 6 residues within 4Å: Chain A: R.118, C.120, C.151, C.211, R.283, F.308 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.120, A:C.151, A:C.211 FES.8: 6 residues within 4Å: Chain B: R.118, C.120, C.151, C.211, R.283, F.308 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.120, B:C.151, B:C.211

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

DTB.4: 12 residues within 4Å: Chain A: L.68, N.174, N.176, P.243, N.245, A.286, F.308, L.313, L.314, T.315, T.316 Ligands: SAM.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.68, A:A.286, A:L.314, A:T.316 Hydrogen bonds: A:N.174, A:N.176, A:N.245, A:N.245, A:T.315, A:T.316, A:T.316 DTB.9: 11 residues within 4Å: Chain B: N.174, N.176, P.243, N.245, A.286, F.308, L.313, L.314, T.315, T.316 Ligands: SAM.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.286, B:L.314, B:T.316 Hydrogen bonds: B:N.174, B:N.176, B:N.245, B:N.245, B:T.315, B:T.316, B:T.316

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 3 residues within 4Å: Chain A: E.289, P.317, E.320 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.289, A:E.320

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Berkovitch, F. et al., Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme. Science (2004)

Release Date

2004-01-13

Peptides

Biotin synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Biotin synthase