- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.36 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x 8AC: 8-aminooctanoic acid(Non-covalent)
- 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
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.36 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x 8AC: 8-aminooctanoic acid(Non-covalent)
- 2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 2 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x GOL: GLYCEROL(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