MolNFT v1 · #70653 · protein
Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase complexed with ribulose-5 phosphate
3LQU: “Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase complexed with ribulose-5 phosphate”. X-ray diffraction, 1 ligand (5SP), 2 pockets (best druggability 0.72). MolNFT v1 #70653 on GenesisL1: 3D structure, binding…
- PDB
- 3LQU
- Type
- protein
- Length
- 403 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
- P66032
- Ligands
- 5SP
- Pockets
- 2 · best druggability 0.72
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 | 205 | 40% helix, 21% strand | P66032 |
| B | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) | protein | 198 | 41% helix, 22% strand | P66032 |
Ligands and binding sites
- 5SP · 5-O-phosphono-D-xylulose · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.72 | 0.94 | 33 | 5SP |
| 2 | 82 | 0.70 | 0.95 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1569 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3LQU · Crystal structure of 3,4-Dihydroxy-2-buta 4-phosphate synthase complexed with Ribulose-5… · the same entry in another collection · chain A against A, 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 B 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 3LQU · PDBe 3LQU · UniProt P66032
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