MolNFT v1 · #61501 · protein
Structure of (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, the terminal enzyme of the non-mevalonate pathway
3DNF · 4-hydroxy-3-methylbut-2-enyl diphosphate reductase: “Structure of (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, the terminal enzyme of the…”. X-ray diffraction, 1 ligand (F3S), 4 pockets (best druggability 0.66). MolNFT…
- PDB
- 3DNF
- Type
- protein
- Length
- 563 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
- O67625
- Ligands
- F3S
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 281 | 46% helix, 19% strand | O67625 |
| B | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 282 | 46% helix, 19% strand | O67625 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.66 | 0.79 | 49 | F3S |
| 2 | 388 | 0.62 | 0.77 | 41 | F3S |
| 3 | 52 | 0.28 | 0.75 | 17 | empty |
| 4 | 53 | 0.25 | 0.72 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 827 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3DNF · Structure of (E)-4-Hydroxy-3-methyl-but-2-enyl Diphosphate Reductase, the Terminal Enzyme… · the same entry in another collection · chain A against A, TM-score 1.00
- O67625 · AlphaFold monomer V2.0 prediction for 4-hydroxy-3-methylbut-2-enyl diphosphate reductase… · a predicted model of the same protein · chain B against A, TM-score 0.83
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 O67625
- Elsewhere: RCSB PDB 3DNF · PDBe 3DNF · UniProt O67625
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