Research workbench
Crystal structure of the isopentenyl phosphate kinase substrate complex
Analyse Crystal structure of the isopentenyl phosphate kinase substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LKK
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-glutamyl kinase related protein
- UniProt
- Q9HLX1
- Ligands
- ATP, IP8
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-glutamyl kinase related protein | protein | 232 | 41% helix, 23% strand | Q9HLX1 |
| B | Gamma-glutamyl kinase related protein | protein | 238 | 38% helix, 23% strand | Q9HLX1 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- IP8 · Isopentenyl phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.57 | 0.78 | 42 | ATP, IP8 |
| 2 | 228 | 0.56 | 0.78 | 43 | ATP, IP8 |
Interfaces
1 interface between chains.
- A–B · 1685 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3LKK · Crystal structure of the isopentenyl phosphate kinase substrate complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HLX1 · AlphaFold monomer V2.0 prediction for isopentenyl phosphate kinase (Q9HLX1) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9HLX1
- Elsewhere: RCSB PDB 3LKK · PDBe 3LKK · UniProt Q9HLX1
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