Research workbench
Crystal structure of mevalonate-3-kinase from thermoplasma acidophilum (mevalonate 3-PHOSPHATE/ADP bound)
Analyse Crystal structure of mevalonate-3-kinase from thermoplasma acidophilum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RKZ
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein TA1305
- UniProt
- Q9HIN1
- Ligands
- 3S4, ADP, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein TA1305 | protein | 313 | 39% helix, 26% strand | Q9HIN1 |
| B | Putative uncharacterized protein TA1305 | protein | 318 | 38% helix, 26% strand | Q9HIN1 |
Ligands and binding sites
- 3S4 · (3R)-5-hydroxy-3-methyl-3-(phosphonooxy)pentanoic acid · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 391 | 0.69 | 0.82 | 50 | empty |
| 2 | 166 | 0.68 | 0.88 | 27 | 3S4 |
| 3 | 228 | 0.64 | 0.83 | 39 | 3S4, SO4 |
| 4 | 76 | 0.44 | 0.81 | 16 | empty |
| 5 | 61 | 0.42 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 675 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4RKZ · Crystal Structure of Mevalonate-3-Kinase from Thermoplasma acidophilum (Mevalonate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HIN1 · AlphaFold monomer V2.0 prediction for mevalonate 3-kinase (Q9HIN1) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q9HIN1
- Elsewhere: RCSB PDB 4RKZ · PDBe 4RKZ · UniProt Q9HIN1
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