SMTL ID : 3qxj.1

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 12 residues within 4Å: Chain A: T.31, N.32, A.33, G.34, K.35, T.36, T.37, K.57, D.72, E.138 Ligands: MG.4, EDO.12 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.32, A:A.33, A:G.34, A:K.35, A:T.36, A:T.36, A:T.37, A:T.37 Water bridges: A:K.35, A:K.35, A:T.36 Salt bridges: A:K.35, A:K.35, A:K.57 GTP.13: 12 residues within 4Å: Chain B: T.31, N.32, A.33, G.34, K.35, T.36, T.37, K.57, D.72, E.138 Ligands: MG.16, EDO.24 15 PLIP interactions: 15 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.37, B:T.37 Water bridges: B:K.35, B:K.35, B:T.36, B:T.36 Salt bridges: B:K.35, B:K.35, B:K.57

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: V.63, N.64, D.65, R.96, Y.97, H.98 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: N.152, L.154, D.155, L.184, H.188 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: N.47, G.50, V.51, K.52, L.83 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: H.22, M.23, K.161, K.163, S.242 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: T.203, S.207 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: L.190, D.191, Y.192, N.222 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: E.109, E.110 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain B: N.30, H.169, N.171 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: K.57, E.60, T.61, A.140 Ligands: GTP.1 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: V.63, N.64, D.65, R.96, Y.97, H.98 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: N.152, L.154, D.155, L.184, H.188 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: N.47, G.50, V.51, K.52, L.83 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: H.22, M.23, K.161, K.163, S.242 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: T.203, S.207 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: L.190, D.191, Y.192, N.222 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: E.109, E.110 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: N.30, H.169, N.171 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: K.57, E.60, T.61, A.140 Ligands: GTP.13 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: T.36, K.57, D.72, E.138 Ligands: GTP.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.36, A:D.72, A:E.138, H2O.6 MG.16: 5 residues within 4Å: Chain B: T.36, K.57, D.72, E.138 Ligands: GTP.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.36, B:D.72, B:E.138, H2O.18

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

NO3.8: 10 residues within 4Å: Chain A: F.25, S.27, A.28, K.35, G.139, A.140, G.141, G.142, L.143, M.153 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.27, A:A.28, A:G.139, A:A.140, A:G.142 Water bridges: A:G.141, A:G.141 NO3.20: 10 residues within 4Å: Chain B: F.25, S.27, A.28, K.35, G.139, A.140, G.141, G.142, L.143, M.153 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.27, B:A.28, B:G.139, B:A.140, B:G.142 Water bridges: B:G.141, B:G.141

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

2011-03-30

Peptides

Dethiobiotin synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Dethiobiotin synthetase

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