Research workbench
Crystal structure of the mevalonate kinase from an archaeon methanosarcina mazei
Analyse Crystal structure of the mevalonate kinase from an archaeon methanosarcina mazei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HAC
- Type
- protein
- Length
- 620 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
- MG
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mevalonate kinase (EC 2.7.1.36) | protein | 312 | 42% helix, 23% strand | Q8PW39 |
| B | Mevalonate kinase (EC 2.7.1.36) | protein | 308 | 44% helix, 23% strand | Q8PW39 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.64 | 0.78 | 43 | empty |
| 2 | 300 | 0.58 | 0.77 | 34 | empty |
| 3 | 143 | 0.47 | 0.77 | 18 | MG |
| 4 | 172 | 0.46 | 0.76 | 19 | empty |
| 5 | 170 | 0.45 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1148 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4HAC · Crystal Structure of the Mevalonate Kinase from an Archaeon Methanosarcina mazei · 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 4HAC · PDBe 4HAC · UniProt Q8PW39
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