Research workbench
ISPH:HMBPP complex after 3 minutes X-ray pre-exposure
Analyse ISPH:HMBPP complex after 3 minutes X-ray pre-exposure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SZO
- 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, H6P
- Pockets
- 8 · 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 | 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
- 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.81 | 0.98 | 26 | SF4, H6P |
| 2 | 131 | 0.79 | 0.97 | 25 | SF4, H6P |
| 3 | 896 | 0.78 | 0.81 | 57 | empty |
| 4 | 150 | 0.55 | 0.82 | 26 | empty |
| 5 | 88 | 0.51 | 0.84 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 937 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3SZO · IspH:HMBPP complex after 3 minutes X-ray pre-exposure · 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 0.99
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 3SZO · PDBe 3SZO · UniProt P62623
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