MolNFT v1 · #81618 · protein
EC_ISPH in complex with 4-oxobutyl diphosphate (1302)
3UWM · 4-hydroxy-3-methylbut-2-enyl diphosphate reductase: “EC_ISPH in complex with 4-oxobutyl diphosphate (1302)”. X-ray diffraction, 3 ligands (SF4, 0K2, 0JX), 7 pockets (best druggability 0.80). MolNFT v1 #81618 on GenesisL1: 3D…
- PDB
- 3UWM
- 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
- P62623
- Ligands
- SF4, 0K2, 0JX
- Pockets
- 7 · best druggability 0.80
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 | 42% helix, 18% strand | P62623 |
| B | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 310 | 43% helix, 18% strand | P62623 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- 0K2 · 4-oxobutyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- 0JX · (3E)-4-hydroxybut-3-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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.80 | 0.98 | 27 | SF4, 0K2, 0JX |
| 2 | 1018 | 0.80 | 0.81 | 61 | empty |
| 3 | 128 | 0.79 | 0.97 | 26 | SF4, 0K2, 0JX |
| 4 | 155 | 0.57 | 0.82 | 28 | empty |
| 5 | 161 | 0.56 | 0.82 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 889 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3UWM · Ec_IspH in complex with 4-oxobutyl diphosphate (1302) · 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 B 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 3UWM · PDBe 3UWM · UniProt P62623
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