Research workbench
Crystal structure of mevalonate-3-kinase from thermoplasma acidophilum (apo form)
Analyse Crystal structure of mevalonate-3-kinase from thermoplasma acidophilum (apo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RKP
- Type
- protein
- Length
- 637 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein TA1305
- UniProt
- Q9HIN1
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.66
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 | 317 | 38% helix, 26% strand | Q9HIN1 |
| B | Putative uncharacterized protein TA1305 | protein | 320 | 37% helix, 26% strand | Q9HIN1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.66 | 0.83 | 41 | SO4, ACT |
| 2 | 559 | 0.66 | 0.77 | 53 | empty |
| 3 | 312 | 0.65 | 0.81 | 46 | SO4, ACT |
Interfaces
1 interface between chains.
- A–B · 258 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4RKP · Crystal Structure of Mevalonate-3-Kinase from Thermoplasma acidophilum (apo form) · the same entry in another collection · chain B against B, 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 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 Q9HIN1
- Elsewhere: RCSB PDB 4RKP · PDBe 4RKP · UniProt Q9HIN1
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