Research workbench
EC_ISPH in complex with 4-oxopentyl diphosphate
Analyse EC_ISPH in complex with 4-oxopentyl diphosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UTD
- 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
- F3S, 0CJ
- 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 | 42% helix, 18% strand | P62623 |
Ligands and binding sites
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B
- 0CJ · 4-oxopentyl 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 | 1111 | 0.80 | 0.82 | 73 | empty |
| 2 | 120 | 0.79 | 0.98 | 25 | F3S, 0CJ |
| 3 | 120 | 0.79 | 0.97 | 26 | F3S, 0CJ |
| 4 | 187 | 0.58 | 0.82 | 34 | empty |
| 5 | 86 | 0.51 | 0.84 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 894 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3UTD · Ec_IspH in complex with 4-oxopentyl diphosphate · 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 3UTD · PDBe 3UTD · UniProt P62623
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