Research workbench
Crystal structure of isopentenyl phosphate kinase from M. jannaschii in complex with ipp
Analyse Crystal structure of isopentenyl phosphate kinase from M. jannaschii in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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