Research workbench
Mevalonate kinase from methanosarcina mazei with 5-phosphomevalonate bound
Analyse Mevalonate kinase from methanosarcina mazei with 5-phosphomevalonate bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MDF
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mevalonate kinase
- EC
- 2.7.1.36
- UniProt
- Q8PW39
- Ligands
- PMV
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mevalonate kinase (EC 2.7.1.36) | protein | 303 | 44% helix, 24% strand | Q8PW39 |
| B | Mevalonate kinase (EC 2.7.1.36) | protein | 301 | 42% helix, 23% strand | Q8PW39 |
Ligands and binding sites
- PMV · (3R)-3-hydroxy-3-methyl-5-(phosphonooxy)pentanoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 13 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 494 | 0.70 | 0.80 | 48 | PMV |
| 2 | 464 | 0.62 | 0.76 | 51 | PMV, GOL |
| 3 | 142 | 0.43 | 0.75 | 22 | GOL |
| 4 | 61 | 0.30 | 0.75 | 15 | GOL |
Interfaces
1 interface between chains.
- A–B · 1207 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6MDF · Mevalonate kinase from Methanosarcina mazei with 5-phosphomevalonate bound · 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 Q8PW39
- Elsewhere: RCSB PDB 6MDF · PDBe 6MDF · UniProt Q8PW39
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