MolNFT v1 · #71588 · protein
Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase domain from mycobacterium tuberculosis at pH 6.00
3MIO: “Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase domain from mycobacterium tuberculosis at…”. X-ray diffraction, 2 ligands (K, PO4), 2 pockets (best druggability 0.62). MolNFT v1 #71588 on GenesisL1: 3D structure…
- PDB
- 3MIO
- Type
- protein
- Length
- 389 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3,4-dihydroxy-2-butanone 4-phosphate synthase
- EC
- 4.1.99.12
- UniProt
- A5U2B7
- Ligands
- K, PO4
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) | protein | 195 | 40% helix, 21% strand | A5U2B7 |
| B | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) | protein | 194 | 40% helix, 22% strand | A5U2B7 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.62 | 0.88 | 19 | empty |
| 2 | 79 | 0.44 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 959 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3MIO · Crystal structure of 3,4-dihydroxy-2-buta 4-phosphate synthase domain from Mycobacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- A5U2B7 · AlphaFold monomer V2.0 prediction for riboflavin biosynthesis protein ribba (A5U2B7) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 A5U2B7
- Elsewhere: RCSB PDB 3MIO · PDBe 3MIO · UniProt A5U2B7
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