MolNFT v1 · #68734 · protein
Crystal structure of isopentenyl phosphate kinase from M. jannaschii in complex with ipp
3K4Y: “Crystal structure of isopentenyl phosphate kinase from M. jannaschii in complex with ipp”. X-ray diffraction, 2 ligands (IPE, SO4), 5 pockets (best druggability 0.57). MolNFT v1 #68734 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3K4Y
- Type
- protein
- Length
- 508 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl phosphate kinase
- UniProt
- Q60352
- Ligands
- IPE, SO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl phosphate kinase | protein | 260 | 40% helix, 24% strand | Q60352 |
| B | Isopentenyl phosphate kinase | protein | 248 | 38% helix, 24% strand | Q60352 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.57 | 0.78 | 48 | IPE, SO4 |
| 2 | 209 | 0.51 | 0.77 | 35 | IPE, SO4 |
| 3 | 86 | 0.40 | 0.78 | 17 | empty |
| 4 | 97 | 0.40 | 0.77 | 18 | empty |
| 5 | 51 | 0.28 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1734 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 3K4Y · Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IPP · the same entry in another collection · chain A against A, TM-score 1.00
- Q60352 · AlphaFold monomer V2.0 prediction for isopentenyl phosphate kinase (Q60352) · 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 Q60352
- Elsewhere: RCSB PDB 3K4Y · PDBe 3K4Y · UniProt Q60352
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