SMTL ID : 3qxx.1

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GDP and 8-aminocaprylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.36 Å

Oligo State

homo-dimer

Ligands

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

8AC.1: 12 residues within 4Å: Chain A: T.31, T.61, S.101, A.102, V.145 Chain B: L.172, G.173, L.174, I.175, N.176 Ligands: MG.3, PO4.5 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.172 Hydrogen bonds: B:G.173, B:I.175, B:N.176, A:T.31, A:T.31 Water bridges: A:K.57 8AC.13: 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, V.145 Ligands: MG.15, PO4.17 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.172 Hydrogen bonds: A:G.173, A:I.175, A:N.176, B:T.31 Water bridges: B:K.57

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.2: 14 residues within 4Å: Chain A: T.31, N.32, A.33, G.34, K.35, T.36, T.37, E.138, N.197, K.199, G.200 Ligands: MG.3, MG.4, PO4.5 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, A:N.197, A:G.200 Water bridges: A:Q.228 Salt bridges: A:K.35 pi-Cation interactions: A:K.199, A:K.199 GDP.14: 14 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, G.200 Ligands: MG.15, MG.16, PO4.17 17 PLIP interactions: 17 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, B:E.138, B:N.197, B:G.200 Water bridges: B:T.36, B:T.36, B:Q.228 Salt bridges: B:K.35 pi-Cation interactions: B:K.199, B:K.199

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.31 Ligands: 8AC.1, GDP.2, MG.4, PO4.5 No protein-ligand interaction detected (PLIP) MG.4: 7 residues within 4Å: Chain A: T.36, K.57, D.72, E.138 Ligands: GDP.2, MG.3, PO4.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.36, A:D.72, A:E.138, H2O.11 MG.15: 5 residues within 4Å: Chain B: T.31 Ligands: 8AC.13, GDP.14, MG.16, PO4.17 No protein-ligand interaction detected (PLIP) MG.16: 7 residues within 4Å: Chain B: T.36, K.57, D.72, E.138 Ligands: GDP.14, MG.15, PO4.17 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.36, B:D.72, B:E.138, H2O.25

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

PO4.5: 11 residues within 4Å: Chain A: T.31, K.35, K.57, D.72, E.138, A.140, G.141 Ligands: 8AC.1, GDP.2, MG.3, MG.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.141 Water bridges: A:N.32, A:K.57, A:K.57 Salt bridges: A:K.35, A:K.57 PO4.17: 11 residues within 4Å: Chain B: T.31, K.35, K.57, D.72, E.138, A.140, G.141 Ligands: 8AC.13, GDP.14, MG.15, MG.16 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:T.31, B:T.31, B:G.141 Water bridges: B:N.32, B:T.36, B:K.57, B:K.57 Salt bridges: B:K.35, B:K.57

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

EDO.6: 6 residues within 4Å: Chain A: V.63, N.64, D.65, R.96, Y.97, H.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.65, A:D.65, A:R.96 Water bridges: A:E.110 EDO.7: 6 residues within 4Å: Chain A: H.22, M.23, K.161, A.162, K.163, S.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.23, A:M.23, A:S.242 Water bridges: A:D.191, A:S.242 EDO.8: 1 residues within 4Å: Chain A: H.206 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: F.94, Y.95, R.96, Y.97, D.111 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.94, A:R.96 Water bridges: A:E.110, A:E.110 EDO.10: 4 residues within 4Å: Chain A: R.40, L.41, Q.44, D.79 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.40, A:D.79 Water bridges: A:R.40, A:R.40, A:Q.44 EDO.11: 3 residues within 4Å: Chain A: Y.95, A.114, P.115 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.95 Water bridges: A:D.117 EDO.18: 6 residues within 4Å: Chain B: V.63, N.64, D.65, R.96, Y.97, H.98 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.65, B:D.65, B:R.96 EDO.19: 6 residues within 4Å: Chain B: H.22, M.23, K.161, A.162, K.163, S.242 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.23, B:M.23, B:S.242 Water bridges: B:S.242 EDO.20: 1 residues within 4Å: Chain B: H.206 No protein-ligand interaction detected (PLIP) EDO.21: 5 residues within 4Å: Chain B: F.94, Y.95, R.96, Y.97, D.111 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.94, B:R.96, B:D.111 Water bridges: B:E.110 EDO.22: 4 residues within 4Å: Chain B: R.40, L.41, Q.44, D.79 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.40, B:D.79 Water bridges: B:R.40, B:R.40, B:Q.44, B:D.79 EDO.23: 3 residues within 4Å: Chain B: Y.95, A.114, P.115 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.95, B:Y.95

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain A: N.152, L.154, D.155, L.184, H.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.152, A:D.155 GOL.24: 5 residues within 4Å: Chain B: N.152, L.154, D.155, L.184, H.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.152, B:D.155

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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