MolNFT v1 · #156725 · protein
Mevalonate kinase from methanosarcina mazei with mevalonate bound
6MDE: “Mevalonate kinase from methanosarcina mazei with mevalonate bound”. X-ray diffraction, 2 ligands (MEV, K), 5 pockets (best druggability 0.71). MolNFT v1 #156725 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6MDE
- Type
- protein
- Length
- 603 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
- MEV, K
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mevalonate kinase (EC 2.7.1.36) | protein | 302 | 45% helix, 25% strand | Q8PW39 |
| B | Mevalonate kinase (EC 2.7.1.36) | protein | 301 | 45% helix, 23% strand | Q8PW39 |
Ligands and binding sites
- MEV · (R)-mevalonate · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 532 | 0.71 | 0.80 | 49 | MEV, K, GOL |
| 2 | 327 | 0.57 | 0.76 | 42 | MEV, GOL |
| 3 | 153 | 0.44 | 0.75 | 23 | empty |
| 4 | 124 | 0.40 | 0.75 | 19 | empty |
| 5 | 108 | 0.40 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1228 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6MDE · Mevalonate kinase from Methanosarcina mazei with mevalonate 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 6MDE · PDBe 6MDE · UniProt Q8PW39
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