MolNFT v1 · #49950 · protein
The biochemical and structural basis for feedback inhibition of mevalonate kinase and isoprenoid metabolism
2R3V: “The biochemical and structural basis for feedback inhibition of mevalonate kinase and isoprenoid metabolism”. X-ray diffraction, 16 pockets (best druggability 0.73). MolNFT v1 #49950 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2R3V
- Type
- protein
- Length
- 1,557 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mevalonate kinase
- EC
- 2.7.1.36
- UniProt
- Q03426
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Mevalonate kinase (EC 2.7.1.36) | protein | 390 | 43% helix, 21% strand | Q03426 |
| B | Mevalonate kinase (EC 2.7.1.36) | protein | 388 | 45% helix, 20% strand | Q03426 |
| D | Mevalonate kinase (EC 2.7.1.36) | protein | 389 | 42% helix, 20% strand | Q03426 |
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 664 | 0.73 | 0.80 | 70 | empty |
| 2 | 1070 | 0.73 | 0.76 | 78 | empty |
| 3 | 527 | 0.70 | 0.79 | 54 | empty |
| 4 | 601 | 0.70 | 0.78 | 59 | empty |
| 5 | 633 | 0.69 | 0.77 | 74 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1023 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 999 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 817 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 810 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 183 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2R3V · The Biochemical and Structural Basis for Feedback Inhibition of Mevalonate Kinase and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q03426 · AlphaFold monomer V2.0 prediction for mevalonate kinase (Q03426) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q03426
- Elsewhere: RCSB PDB 2R3V · PDBe 2R3V · UniProt Q03426
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