Research workbench
Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with sulfate ion.
Analyse Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LRJ
- Type
- protein
- Length
- 794 residues
- Chains
- 4
- 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
- P66032
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 4 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 | 199 | 40% helix, 22% strand | P66032 |
| B | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) | protein | 198 | 40% helix, 22% strand | P66032 |
| C | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) | protein | 198 | 40% helix, 22% strand | P66032 |
| D | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) | protein | 199 | 40% helix, 22% strand | P66032 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.71 | 0.77 | 93 | SO4 |
| 2 | 187 | 0.65 | 0.85 | 32 | SO4 |
| 3 | 153 | 0.64 | 0.86 | 30 | SO4 |
| 4 | 153 | 0.63 | 0.86 | 29 | SO4 |
| 5 | 63 | 0.59 | 0.90 | 19 | SO4 |
Interfaces
5 interfaces between chains.
- A–B · 1555 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1542 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 267 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LRJ · Crystal structure of 3,4-Dihydroxy-2-buta 4-phosphate synthase in complex with sulfate… · the same entry in another collection · chain D against D, TM-score 1.00
- P66032 · AlphaFold monomer V2.0 prediction for 3,4-dihydroxy-2-butanone 4-phosphate synthase… · a predicted model of the same protein · chain D 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 P66032
- Elsewhere: RCSB PDB 3LRJ · PDBe 3LRJ · UniProt P66032
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.