- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-trimer
- Ligands
- 2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)
C5P.3: 14 residues within 4Å:- Chain A: S.321, P.324, K.325, I.326, T.327, K.330, A.352, T.353, T.354, E.356
- Chain C: D.277, I.278, G.279, E.280
12 PLIP interactions:10 interactions with chain A, 2 interactions with chain C- Hydrophobic interactions: A:T.354
- Hydrogen bonds: A:S.321, A:I.326, A:T.327, A:T.327, A:K.330, A:T.353, A:T.354, A:E.356, A:E.356, C:D.277, C:G.279
C5P.11: 13 residues within 4Å:- Chain B: D.277, G.279, E.280
- Chain C: S.321, P.324, K.325, I.326, T.327, K.330, A.352, T.353, T.354, E.356
13 PLIP interactions:11 interactions with chain C, 2 interactions with chain B- Hydrophobic interactions: C:T.354
- Hydrogen bonds: C:S.321, C:I.326, C:T.327, C:T.327, C:K.330, C:T.354, C:E.356, C:E.356, C:E.356, B:D.277, B:G.279
- Water bridges: C:T.353
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 7 residues within 4Å:- Chain A: D.105, R.108, I.156, T.158, K.177, D.178, K.202
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.105, A:R.108, A:R.108, A:I.156
GOL.12: 6 residues within 4Å:- Chain A: K.220, T.222
- Chain B: K.220, T.222
- Chain C: K.220, T.222
12 PLIP interactions:3 interactions with chain C, 4 interactions with chain A, 5 interactions with chain B- Hydrogen bonds: C:T.222, C:T.222, C:T.222, A:K.220, B:K.220
- Water bridges: A:T.222, A:T.222, A:T.222, B:T.222, B:T.222, B:T.222, B:T.222
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)
CDP.8: 18 residues within 4Å:- Chain A: H.231, D.277, I.278, G.279, E.280, D.284
- Chain B: S.321, P.324, K.325, I.326, T.327, K.330, A.352, T.353, T.354, E.356
- Ligands: EDO.1, ZN.5
13 PLIP interactions:3 interactions with chain A, 10 interactions with chain B- Hydrogen bonds: A:D.277, A:G.279, B:S.321, B:I.326, B:T.327, B:T.327, B:K.330, B:T.354, B:T.354, B:E.356
- Salt bridges: A:H.231
- Hydrophobic interactions: B:A.352, B:T.354
- 1 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Chen, X. et al., Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes. Int J Antimicrob Agents (2024)
- Release Date
- 2024-04-10
- Peptides
- Bifunctional enzyme IspD/IspF: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DB
EC
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.50 Å
- Oligo State
- homo-trimer
- Ligands
- 2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 3 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)
- 2 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)
- 1 x SO4: SULFATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Chen, X. et al., Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes. Int J Antimicrob Agents (2024)
- Release Date
- 2024-04-10
- Peptides
- Bifunctional enzyme IspD/IspF: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DB
EC
F