MolNFT v1 · #100354 · protein
Isph in complex with pyridin-2-ylmethyl diphosphate
4MV0 · 4-hydroxy-3-methylbut-2-enyl diphosphate reductase: “Isph in complex with pyridin-2-ylmethyl diphosphate”. X-ray diffraction, 2 ligands (F3S, 2E6), 9 pockets (best druggability 0.81). MolNFT v1 #100354 on GenesisL1: 3D structure…
- PDB
- 4MV0
- Type
- protein
- Length
- 619 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
- C9QSC3
- Ligands
- F3S, 2E6
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 309 | 41% helix, 18% strand | C9QSC3 |
| B | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 310 | 42% helix, 18% strand | C9QSC3 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B
- 2E6 · pyridin-2-ylmethyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.81 | 0.97 | 27 | F3S, 2E6 |
| 2 | 938 | 0.79 | 0.81 | 58 | empty |
| 3 | 121 | 0.78 | 0.97 | 25 | F3S, 2E6 |
| 4 | 276 | 0.59 | 0.79 | 33 | empty |
| 5 | 98 | 0.48 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 847 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4MV0 · IspH in complex with pyridin-2-ylmethyl diphosphate · the same entry in another collection · chain A against A, TM-score 1.00
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 C9QSC3
- Elsewhere: RCSB PDB 4MV0 · PDBe 4MV0 · UniProt C9QSC3
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