Research workbench
Ribb from vibrio cholera bound with intermediate 2 in the reaction cycle and the products dhbp and formate
Analyse Ribb from vibrio cholera bound with intermediate 2 in the reaction cycle and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UF5
- Type
- protein
- Length
- 208 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
- N52, N4O, MN
- Pockets
- 1 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) | protein | 208 | 41% helix, 21% strand | A0A0H6NPW4 |
Ligands and binding sites
- N52 · (2R)-2-(dihydroxymethyl)-2-hydroxy-3-oxobutyl dihydrogen phosphate · ligand · chains A
- N4O · (2R)-2-hydroxy-3-oxobutyl dihydrogen phosphate · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- FMT · Formic acid · additive · 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 | 73 | 0.38 | 0.78 | 19 | N52, N4O, MN |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 7UF5 · RibB from Vibrio cholera bound with intermediate 2 in the reaction cycle and the products… · 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 7UF5 · PDBe 7UF5 · UniProt A0A0H6NPW4
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