Research workbench
3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii
Analyse 3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PVW
- Type
- protein
- Length
- 657 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3,4-dihydroxy-2-butanone 4-phosphate synthase
- EC
- 5.4.99.-
- UniProt
- Q60364
- Ligands
- ZN, CA, PO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 5.4.99.-) | protein | 219 | 43% helix, 21% strand | Q60364 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.79 | 0.93 | 38 | empty |
| 2 | 117 | 0.78 | 0.97 | 30 | ZN, CA, PO4 |
| 3 | 81 | 0.74 | 0.96 | 25 | empty |
| 4 | 486 | 0.63 | 0.76 | 41 | empty |
| 5 | 125 | 0.53 | 0.81 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2633 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 144 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 77 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1PVW · 3,4-dihydroxy-2-buta 4-phosphate synthase from M. jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
- Q60364 · AlphaFold monomer V2.0 prediction for 3,4-dihydroxy-2-butanone 4-phosphate synthase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q60364
- Elsewhere: RCSB PDB 1PVW · PDBe 1PVW · UniProt Q60364
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