MolNFT v1 · #188814 · protein
Ribb from vibrio cholera bound with intermediate 1 of the reaction cycle and D-ribulose-5-phosphate (D-RU5P)
7UF4 · 3,4-dihydroxy-2-butanone 4-phosphate synthase: “Ribb from vibrio cholera bound with intermediate 1 of the reaction cycle and D-ribulose-5-phosphate (D-RU5P)”. X-ray diffraction, 3 ligands (N46, 5RP, MN), 1 pocket (best druggability…
- PDB
- 7UF4
- Type
- protein
- Length
- 216 residues
- Chains
- 1
- 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
- A0A0H6NPW4
- Ligands
- N46, 5RP, MN
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) | protein | 216 | 40% helix, 20% strand | A0A0H6NPW4 |
Ligands and binding sites
- N46 · (2R)-2-hydroxy-3,4-dioxopentyl dihydrogen phosphate · ligand · chains A
- 5RP · Ribulose-5-phosphate · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.50 | 0.86 | 17 | N46, 5RP, MN |
Compared structures
- 7UF4 · RibB from Vibrio cholera bound with intermediate 1 of the reaction cycle and… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0H6NPW4
- Elsewhere: RCSB PDB 7UF4 · PDBe 7UF4 · UniProt A0A0H6NPW4
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