SMTL ID : 3qxc.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.34 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 14 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, N.197, K.199, Q.228 Ligands: MG.2 22 PLIP interactions: 22 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:N.197, A:Q.228 Water bridges: A:T.31, A:K.35, A:K.57, A:K.57, A:G.200, A:G.200, A:G.200 Salt bridges: A:K.35, A:K.35, A:K.57 pi-Cation interactions: A:K.199 ATP.18: 14 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, N.197, K.199, Q.228 Ligands: MG.19 24 PLIP interactions: 24 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:N.197, B:N.197, B:Q.228 Water bridges: B:T.31, B:K.35, B:T.36, B:T.36, B:K.57, B:K.57, B:G.200, B:G.200, B:G.200 Salt bridges: B:K.35, B:K.35, B:K.57 pi-Cation interactions: B:K.199

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.36, K.57, D.72, E.138 Ligands: ATP.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.5 MG.19: 5 residues within 4Å: Chain B: T.36, K.57, D.72, E.138 Ligands: ATP.18 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)

NO3.3: 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:K.35, 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:K.35, B:A.140, B:G.142 Water bridges: B:G.141, B:G.141

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

EDO.4: 6 residues within 4Å: Chain A: N.152, L.154, D.155, L.184, H.188 Ligands: EDO.28 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: V.63, N.64, D.65, R.96, Y.97, H.98 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: N.47, G.50, V.51, K.52, L.83 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: H.22, M.23, K.161, K.163, S.242 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: R.40, L.41, Q.44, D.79 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: N.201, N.202, T.203, A.204 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: N.30, H.169, N.171 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: L.179, D.182, F.183, K.186 Ligands: EDO.21 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: L.190, D.191, Y.192, N.222 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: L.210, I.213, E.214, N.217, I.224, V.225, I.226 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: T.31, T.61, G.62, V.100, S.101 Chain B: L.172 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: F.94, Y.95, R.96, Y.97, D.111 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: N.152, L.154, D.155, L.184, H.188 Ligands: EDO.11 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: V.63, N.64, D.65, R.96, Y.97, H.98 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: N.47, G.50, V.51, K.52, L.83 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: H.22, M.23, K.161, K.163, S.242 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: R.40, L.41, Q.44, D.79 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: N.201, N.202, T.203, A.204 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain B: N.30, H.169, N.171 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: L.179, D.182, F.183, K.186 Ligands: EDO.4 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: L.190, D.191, Y.192, N.222 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain B: L.210, I.213, E.214, N.217, I.224, V.225, I.226 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain A: L.172 Chain B: T.31, T.61, G.62, V.100, S.101 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: F.94, Y.95, R.96, Y.97, D.111 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 7 residues within 4Å: Chain A: C.144, P.146, E.151, N.152, D.155 Chain B: L.179, Y.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.144, A:N.152, A:D.155 GOL.30: 7 residues within 4Å: Chain A: L.179, Y.212 Chain B: C.144, P.146, E.151, N.152, D.155 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:Y.212, A:Y.212 Hydrogen bonds: B:C.144, B:N.152, B:D.155

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.16: 2 residues within 4Å: Chain A: H.206, S.207 No protein-ligand interaction detected (PLIP) PEG.33: 2 residues within 4Å: Chain B: H.206, S.207 No protein-ligand interaction detected (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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