SMTL ID : 8vdw.1

X-Ray Crystal Structure of the biotin synthase from V. parvula

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

homo-dimer

Ligands

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

Q46.1: 10 residues within 4Å: Chain A: C.91, R.143, S.145, C.178, R.199, H.201, C.238, R.308, M.333 Ligands: DTB.4 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.91, A:C.178, A:C.238 Q46.6: 10 residues within 4Å: Chain B: C.91, I.93, R.143, S.145, C.178, H.201, C.238, R.308, M.333 Ligands: DTB.7 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.91, B:C.178, B:C.238

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

SAM.2: 18 residues within 4Å: Chain A: F.107, T.148, G.150, S.180, G.182, H.201, N.203, E.205, K.223, I.242, N.270, I.271, L.272, N.273, V.275, L.338 Ligands: SF4.3, DTB.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.150, A:G.182, A:N.203, A:E.205, A:N.273, A:N.273 Water bridges: A:T.148, A:H.201, A:K.223, A:K.223, A:K.223, A:K.223 Salt bridges: A:K.223 pi-Stacking: A:F.107 SAM.9: 19 residues within 4Å: Chain B: F.107, V.147, T.148, G.150, S.180, G.182, H.201, N.203, E.205, K.223, I.242, N.270, I.271, L.272, N.273, V.275, L.338 Ligands: DTB.7, SF4.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.150, B:S.180, B:G.182, B:N.203, B:E.205, B:N.273, B:N.273 Water bridges: B:H.201, B:N.203, B:K.223 Salt bridges: B:K.223 pi-Stacking: B:F.107

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

SF4.3: 9 residues within 4Å: Chain A: C.101, E.103, C.105, F.107, C.108, S.149, G.150, H.218 Ligands: SAM.2 4 PLIP interactions: 4 interactions with chain A, Salt bridges: A:E.205 Metal complexes: A:C.101, A:C.105, A:C.108 SF4.8: 10 residues within 4Å: Chain B: C.101, E.103, C.105, F.107, C.108, S.111, S.149, G.150, H.218 Ligands: SAM.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Salt bridges: B:E.103 Metal complexes: B:C.101, B:C.105, B:C.108, SAM.9

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

DTB.4: 13 residues within 4Å: Chain A: I.93, H.201, N.203, P.268, N.270, A.310, M.333, Y.337, L.338, T.339, T.340 Ligands: Q46.1, SAM.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.93, A:Y.337, A:L.338 Hydrogen bonds: A:H.201, A:N.203, A:N.270, A:N.270, A:L.338, A:T.339, A:T.340 DTB.7: 12 residues within 4Å: Chain B: I.93, H.201, N.203, P.268, N.270, M.333, Y.337, L.338, T.339, T.340 Ligands: Q46.6, SAM.9 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.93, B:Y.337, B:L.338 Hydrogen bonds: B:H.201, B:N.203, B:N.270, B:N.270, B:L.338, B:T.339, B:T.340, B:T.340

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 7 residues within 4Å: Chain A: D.77, R.80, L.325, K.326, G.327, G.328, L.329 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.77, A:R.80, A:G.328, A:L.329

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Biotin synthase