Research workbench
Crystal structure of ISPH:IPP complex
Analyse Crystal structure of ISPH:IPP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KEM
- 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
- IPE, F3S
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% 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 | 41% helix, 17% strand | P62623 |
| B | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 310 | 41% helix, 17% strand | P62623 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- F3S · FE3-S4 cluster · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.81 | 0.98 | 28 | IPE, F3S |
| 2 | 125 | 0.81 | 0.98 | 27 | IPE, F3S |
| 3 | 725 | 0.69 | 0.77 | 65 | empty |
| 4 | 63 | 0.32 | 0.76 | 17 | empty |
| 5 | 54 | 0.30 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 359 Ų buried · 4 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 3KEM · PDBe 3KEM · UniProt P62623
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.