SMTL ID : 3fpa.2 (2 other biounits)

Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase complexed with dethiobiotin and phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 9 residues within 4Å: Chain A: T.36, G.37, V.38, G.39, K.40, T.41, E.133 Ligands: PO4.2, MG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.37, A:V.38, A:G.39, A:K.40, A:T.41 Water bridges: A:V.42 Salt bridges: A:K.40 PO4.2: 11 residues within 4Å: Chain A: T.36, K.40, K.62, D.74, E.133, G.134, A.135, G.136 Ligands: PO4.1, MG.4, DTB.7 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.36, A:D.74, A:G.136 Water bridges: A:K.62 Salt bridges: A:K.40, A:K.62 PO4.5: 12 residues within 4Å: Chain B: T.36, K.40, T.41, K.62, D.74, E.133, G.134, A.135, G.136 Ligands: DTB.3, PO4.6, MG.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:T.36, B:T.36, B:D.74, B:E.133, B:G.136 Water bridges: B:K.62, B:T.66, B:D.74 Salt bridges: B:K.40, B:K.62 PO4.6: 9 residues within 4Å: Chain B: T.36, G.37, V.38, G.39, K.40, T.41, E.133 Ligands: PO4.5, MG.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.36, B:G.37, B:V.38, B:G.39, B:K.40, B:T.41 Water bridges: B:V.42 Salt bridges: B:K.40

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

DTB.3: 15 residues within 4Å: Chain A: L.168, G.169, T.170, L.171, N.172, N.207 Chain B: T.36, T.66, R.70, M.97, A.98, A.135, G.136, V.140 Ligands: PO4.5 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:A.98, B:A.135, A:L.168 Hydrogen bonds: B:T.66, B:R.70, A:G.169, A:L.171, A:N.172 Water bridges: B:K.62, B:T.66 DTB.7: 14 residues within 4Å: Chain A: T.36, T.66, R.70, D.72, P.96, M.97, A.98, V.140 Chain B: L.168, G.169, T.170, L.171, N.172 Ligands: PO4.2 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:T.36, A:A.98, A:V.140 Hydrogen bonds: A:T.36, A:T.36, A:R.70, A:D.72, B:G.169, B:L.171, B:N.172 Water bridges: B:N.172

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: T.41, D.74, E.133 Ligands: PO4.1, PO4.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.41, A:D.74, A:E.133 MG.8: 5 residues within 4Å: Chain B: T.41, D.74, E.133 Ligands: PO4.5, PO4.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.41, B:D.74, B:E.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dey, S. et al., Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase. Biochemistry (2010)

Release Date

2009-06-30

Peptides

Dethiobiotin synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Dethiobiotin synthetase

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