Research workbench
Structure of active isph shows a novel fold with a [3FE-4S] cluster in the catalytic centre
Analyse Structure of active isph shows a novel fold with a [3FE-4S] cluster in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F7T
- Type
- protein
- Length
- 620 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
- EC
- 1.17.1.2
- UniProt
- P62623
- Ligands
- F3S, POP, PO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 310 | 42% helix, 18% strand | P62623 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.81 | 0.82 | 87 | PO4 |
| 2 | 137 | 0.81 | 0.98 | 30 | F3S, POP |
| 3 | 132 | 0.80 | 0.98 | 26 | F3S, POP |
| 4 | 169 | 0.56 | 0.81 | 27 | empty |
| 5 | 143 | 0.39 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 861 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3F7T · Structure of active IspH shows a novel fold with a [3Fe-4S] cluster in the catalytic… · the same entry in another collection · chain A against A, TM-score 1.00
- P62623 · AlphaFold monomer V2.0 prediction for 4-hydroxy-3-methylbut-2-enyl diphosphate reductase… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P62623
- Elsewhere: RCSB PDB 3F7T · PDBe 3F7T · UniProt P62623
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