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

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori cocrystallized with ATP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 11 residues within 4Å: Chain A: T.31, K.35, K.57, D.72, E.138, A.140, G.141 Ligands: MG.2, PO4.4, ADP.6, 8AC.10 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.31, A:T.31, A:T.36, A:G.141 Salt bridges: A:K.35, A:K.57 PO4.4: 10 residues within 4Å: Chain A: T.31, N.32, A.33, G.34, K.35, T.36, E.138 Ligands: PO4.1, MG.2, ADP.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.31, A:N.32, A:A.33, A:G.34, A:K.35, A:T.36, A:T.36, A:E.138 Salt bridges: A:K.35 PO4.7: 11 residues within 4Å: Chain B: T.31, K.35, K.57, D.72, E.138, A.140, G.141 Ligands: 8AC.5, MG.8, PO4.9, ADP.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.31, B:T.31, B:N.32, B:T.36, B:E.138, B:G.141 Salt bridges: B:K.35, B:K.57 PO4.9: 10 residues within 4Å: Chain B: T.31, N.32, A.33, G.34, K.35, T.36, E.138 Ligands: PO4.7, MG.8, ADP.11 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.31, B:N.32, B:A.33, B:G.34, B:K.35, B:T.36, B:T.36 Salt bridges: B:K.35

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: T.36, K.57, D.72, E.138 Ligands: PO4.1, PO4.4, ADP.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.36, A:D.72, A:E.138 MG.8: 7 residues within 4Å: Chain B: T.36, K.57, D.72, E.138 Ligands: PO4.7, PO4.9, ADP.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.36, B:D.72, B:E.138

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 6 residues within 4Å: Chain A: V.63, N.64, D.65, R.96, Y.97, H.98 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.65, A:D.65

2 x 8AC: 8-aminooctanoic acid(Non-covalent)

8AC.5: 12 residues within 4Å: Chain A: L.172, G.173, L.174, I.175, N.176 Chain B: T.31, T.61, S.101, A.102, G.141, V.145 Ligands: PO4.7 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.172, B:A.102, B:V.145 Hydrogen bonds: A:G.173, A:L.174, A:I.175, A:N.176 8AC.10: 12 residues within 4Å: Chain A: T.31, T.61, S.101, A.102, G.141, V.145 Chain B: L.172, G.173, L.174, I.175, N.176 Ligands: PO4.1 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.102, A:V.145, B:L.172 Hydrogen bonds: A:T.61, B:G.173, B:I.175, B:N.176

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.6: 13 residues within 4Å: Chain A: N.32, A.33, G.34, K.35, T.36, T.37, D.72, E.138, N.197, Q.228 Ligands: PO4.1, MG.2, PO4.4 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.31, A:T.31, A:N.32, A:A.33, A:G.34, A:G.34, A:K.35, A:T.36, A:T.36, A:T.37, A:T.37, A:N.197, A:N.197 Salt bridges: A:K.35 ADP.11: 13 residues within 4Å: Chain B: T.31, N.32, A.33, G.34, K.35, T.36, T.37, E.138, N.197, K.199 Ligands: PO4.7, MG.8, PO4.9 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:T.31, B:T.31, B:N.32, B:A.33, B:G.34, B:G.34, B:K.35, B:T.36, B:T.36, B:T.37, B:T.37, B:N.197, B:N.197, B:K.199, B:Q.228 Salt bridges: B:K.35 pi-Cation interactions: B:K.199, B:K.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porebski, P.J. et al., Structural characterization of Helicobacter pylori dethiobiotin synthetase reveals differences between family members. Febs J. (2012)

Release Date

2010-05-19

Peptides

Dethiobiotin synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Dethiobiotin synthetase

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