MolNFT v1 · #38991 · protein
Crystal structure of L. major mevalonate kinase in complex with R-mevalonate
2HFU · Mevalonate kinase, putative: “Crystal structure of L. major mevalonate kinase in complex with R-mevalonate”. X-ray diffraction, 1 ligand (MEV), 6 pockets (best druggability 0.75). MolNFT v1 #38991 on GenesisL1: 3D structure, binding…
- PDB
- 2HFU
- Type
- protein
- Length
- 651 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mevalonate kinase, putative
- EC
- 2.7.1.36
- UniProt
- Q4Q6K7
- Ligands
- MEV
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mevalonate kinase, putative (EC 2.7.1.36) | protein | 326 | 43% helix, 25% strand | Q4Q6K7 |
| B | Mevalonate kinase, putative (EC 2.7.1.36) | protein | 325 | 44% helix, 25% strand | Q4Q6K7 |
Ligands and binding sites
- MEV · (R)-mevalonate · ligand · chains A
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 | 399 | 0.75 | 0.85 | 48 | MEV |
| 2 | 476 | 0.74 | 0.83 | 48 | empty |
| 3 | 138 | 0.72 | 0.92 | 31 | empty |
| 4 | 144 | 0.44 | 0.76 | 26 | empty |
| 5 | 82 | 0.39 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1081 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2HFU · Crystal structure of L. major mevalonate kinase in complex with R-mevalonate · the same entry in another collection · 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 Q4Q6K7
- Elsewhere: RCSB PDB 2HFU · PDBe 2HFU · UniProt Q4Q6K7
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