MolNFT v1 · #79344 · protein
ISPH:HMBPP (substrate) structure of the E126D mutant
3T0F · 4-hydroxy-3-methylbut-2-enyl diphosphate reductase: “ISPH:HMBPP (substrate) structure of the E126D mutant”. X-ray diffraction, 2 ligands (F3S, H6P), 6 pockets (best druggability 0.80). MolNFT v1 #79344 on GenesisL1: 3D structure…
- PDB
- 3T0F
- Type
- protein
- Length
- 618 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, H6P
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 314 | 41% helix, 19% strand | P62623 |
| B | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 304 | 40% helix, 20% strand | P62623 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B
- H6P · (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate · ligand · 2 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 | 160 | 0.80 | 0.96 | 29 | F3S, H6P |
| 2 | 1169 | 0.78 | 0.80 | 68 | empty |
| 3 | 307 | 0.71 | 0.84 | 44 | F3S, H6P |
| 4 | 527 | 0.67 | 0.78 | 51 | empty |
| 5 | 182 | 0.43 | 0.73 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3T0F · IspH:HMBPP (substrate) structure of the E126D mutant · 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 0.97
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 3T0F · PDBe 3T0F · UniProt P62623
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