SMTL ID : 3qy0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

GDP.1: 11 residues within 4Å: Chain A: T.31, N.32, A.33, G.34, K.35, T.36, T.37, E.138 Ligands: PO4.2, MG.3, MG.4 8 PLIP interactions: 8 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 Salt bridges: A:K.35 GDP.21: 11 residues within 4Å: Chain B: T.31, N.32, A.33, G.34, K.35, T.36, T.37, E.138 Ligands: PO4.22, MG.23, MG.24 11 PLIP interactions: 11 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:T.36, B:T.36 Salt bridges: B:K.35

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

PO4.2: 10 residues within 4Å: Chain A: T.31, K.35, K.57, D.72, E.138, A.140, G.141 Ligands: GDP.1, MG.3, MG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.141 Water bridges: A:N.32, A:K.57 Salt bridges: A:K.35, A:K.57 PO4.22: 10 residues within 4Å: Chain B: T.31, K.35, K.57, D.72, E.138, A.140, G.141 Ligands: GDP.21, MG.23, MG.24 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.31, B:G.141 Water bridges: B:N.32, B:T.36, B:K.57 Salt bridges: B:K.35, B:K.57

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.31, N.32 Ligands: GDP.1, PO4.2, MG.4 No protein-ligand interaction detected (PLIP) MG.4: 7 residues within 4Å: Chain A: T.36, K.57, D.72, E.138 Ligands: GDP.1, PO4.2, MG.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.36, A:D.72, A:E.138, H2O.2 MG.23: 5 residues within 4Å: Chain B: T.31, N.32 Ligands: GDP.21, PO4.22, MG.24 No protein-ligand interaction detected (PLIP) MG.24: 7 residues within 4Å: Chain B: T.36, K.57, D.72, E.138 Ligands: GDP.21, PO4.22, MG.23 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.36, B:D.72, B:E.138, H2O.10

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

EDO.5: 5 residues within 4Å: Chain A: N.152, L.154, D.155, L.184 Ligands: EDO.19 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: F.94, Y.95, R.96, Y.97, D.111 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: H.206, S.207 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: T.61, S.101, A.102, P.103, A.140, G.141, V.145 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: K.161, A.162, K.163, L.190, D.191 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: N.217, I.226, Q.229 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: V.63, N.64, D.65, R.96, Y.97, H.98 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: T.29, N.30, T.31, G.141 Chain B: G.173, N.176, D.177 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: N.47, G.50, V.51, K.52, L.83 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: R.40, L.41, Q.44, D.79 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: Y.95, A.114, P.115, D.117 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: H.22, M.23, K.161, K.163, K.240, S.242 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: L.179, Y.212 Chain B: C.144, E.151, N.152, D.155 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: F.19, H.22, L.239, G.241 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: L.179, D.182, F.183, K.186 Ligands: EDO.5 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: D.111, P.112, N.113 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: N.152, L.154, D.155, L.184 Ligands: EDO.39 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: F.94, Y.95, R.96, Y.97, D.111 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain B: H.206, S.207 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain B: T.61, S.101, A.102, P.103, A.140, G.141, V.145 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: K.161, A.162, K.163, L.190, D.191 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: N.217, I.226, Q.229 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain B: V.63, N.64, D.65, R.96, Y.97, H.98 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain A: G.173, N.176, D.177 Chain B: T.29, N.30, T.31, G.141 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: N.47, G.50, V.51, K.52, L.83 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain B: R.40, L.41, Q.44, D.79 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain B: Y.95, A.114, P.115, D.117 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: H.22, M.23, K.161, K.163, K.240, S.242 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain A: C.144, E.151, N.152, D.155 Chain B: L.179, Y.212 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: F.19, H.22, L.239, G.241 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain A: L.179, D.182, F.183, K.186 Ligands: EDO.25 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain B: D.111, P.112, N.113 Ligand excluded by PLIP

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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