Research workbench
Crystal structure of ISPH:HMBPP-complex
Analyse Crystal structure of ISPH:HMBPP-complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KE8
- 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, EIP
- Pockets
- 7 · 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 | 42% helix, 18% strand | P62623 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- EIP · 4-hydroxy-3-methyl butyl 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 | 137 | 0.81 | 0.98 | 26 | SF4, EIP |
| 2 | 133 | 0.80 | 0.97 | 26 | SF4, EIP |
| 3 | 568 | 0.76 | 0.83 | 54 | empty |
| 4 | 88 | 0.52 | 0.84 | 17 | empty |
| 5 | 73 | 0.50 | 0.85 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 915 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 3KE8 · PDBe 3KE8 · UniProt P62623
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