- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.34 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 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 PLIPEDO.5: 6 residues within 4Å:- Chain A: V.63, N.64, D.65, R.96, Y.97, H.98
Ligand excluded by PLIPEDO.6: 5 residues within 4Å:- Chain A: N.47, G.50, V.51, K.52, L.83
Ligand excluded by PLIPEDO.7: 5 residues within 4Å:- Chain A: H.22, M.23, K.161, K.163, S.242
Ligand excluded by PLIPEDO.8: 4 residues within 4Å:- Chain A: R.40, L.41, Q.44, D.79
Ligand excluded by PLIPEDO.9: 4 residues within 4Å:- Chain A: N.201, N.202, T.203, A.204
Ligand excluded by PLIPEDO.10: 3 residues within 4Å:- Chain A: N.30, H.169, N.171
Ligand excluded by PLIPEDO.11: 5 residues within 4Å:- Chain A: L.179, D.182, F.183, K.186
- Ligands: EDO.21
Ligand excluded by PLIPEDO.12: 4 residues within 4Å:- Chain A: L.190, D.191, Y.192, N.222
Ligand excluded by PLIPEDO.14: 7 residues within 4Å:- Chain A: L.210, I.213, E.214, N.217, I.224, V.225, I.226
Ligand excluded by PLIPEDO.15: 6 residues within 4Å:- Chain A: T.31, T.61, G.62, V.100, S.101
- Chain B: L.172
Ligand excluded by PLIPEDO.17: 5 residues within 4Å:- Chain A: F.94, Y.95, R.96, Y.97, D.111
Ligand excluded by PLIPEDO.21: 6 residues within 4Å:- Chain B: N.152, L.154, D.155, L.184, H.188
- Ligands: EDO.11
Ligand excluded by PLIPEDO.22: 6 residues within 4Å:- Chain B: V.63, N.64, D.65, R.96, Y.97, H.98
Ligand excluded by PLIPEDO.23: 5 residues within 4Å:- Chain B: N.47, G.50, V.51, K.52, L.83
Ligand excluded by PLIPEDO.24: 5 residues within 4Å:- Chain B: H.22, M.23, K.161, K.163, S.242
Ligand excluded by PLIPEDO.25: 4 residues within 4Å:- Chain B: R.40, L.41, Q.44, D.79
Ligand excluded by PLIPEDO.26: 4 residues within 4Å:- Chain B: N.201, N.202, T.203, A.204
Ligand excluded by PLIPEDO.27: 3 residues within 4Å:- Chain B: N.30, H.169, N.171
Ligand excluded by PLIPEDO.28: 5 residues within 4Å:- Chain B: L.179, D.182, F.183, K.186
- Ligands: EDO.4
Ligand excluded by PLIPEDO.29: 4 residues within 4Å:- Chain B: L.190, D.191, Y.192, N.222
Ligand excluded by PLIPEDO.31: 7 residues within 4Å:- Chain B: L.210, I.213, E.214, N.217, I.224, V.225, I.226
Ligand excluded by PLIPEDO.32: 6 residues within 4Å:- Chain A: L.172
- Chain B: T.31, T.61, G.62, V.100, S.101
Ligand excluded by PLIPEDO.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)
- 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
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.34 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x NO3: NITRATE ION(Non-functional Binders)
- 24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 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
AB
A