- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-trimer
- Ligands
- 7 x GOL: GLYCEROL(Non-functional Binders)
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.4: 4 residues within 4Å:- Chain A: R.85, R.108, I.156, K.177
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.85, A:R.108, A:R.108, A:I.156
EDO.5: 6 residues within 4Å:- Chain A: L.135, P.136, C.137, Y.138, D.139, L.155
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.138, A:D.139, A:D.139
EDO.6: 4 residues within 4Å:- Chain A: H.263, I.278, F.282, D.284
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.256, A:S.256
EDO.7: 1 residues within 4Å:- Chain A: Y.129
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.129
EDO.11: 3 residues within 4Å:- Chain A: E.344
- Chain B: H.37, T.38
1 PLIP interactions:1 interactions with chain A- Water bridges: A:S.346
EDO.12: 4 residues within 4Å:- Chain B: E.46, K.49, E.75, I.76
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.46, B:E.46
EDO.17: 7 residues within 4Å:- Chain C: R.85, D.105, R.108, I.156, T.158, K.177, D.178
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:D.105
EDO.18: 3 residues within 4Å:- Chain C: D.247, P.328, Y.329
No protein-ligand interaction detected (PLIP)- 1 x SO4: SULFATE ION(Non-functional Binders)
- 3 x ZN: ZINC ION(Non-covalent)
ZN.9: 3 residues within 4Å:- Chain A: D.229, H.231, H.263
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.229, A:D.229, A:H.231, A:H.263, H2O.5
ZN.13: 3 residues within 4Å:- Chain B: D.229, H.231, H.263
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.229, B:D.229, B:H.231, B:H.263, H2O.10
ZN.19: 3 residues within 4Å:- Chain C: D.229, H.231, H.263
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:D.229, C:D.229, C:H.231, C:H.263, H2O.15
- 1 x CL: CHLORIDE 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
AB
BC
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.40 Å
- Oligo State
- homo-trimer
- Ligands
- 7 x GOL: GLYCEROL(Non-functional Binders)
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x SO4: SULFATE ION(Non-functional Binders)
- 3 x ZN: ZINC ION(Non-covalent)
- 1 x CL: CHLORIDE 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
AB
BC
C