Research workbench
Structure of ribb complexed with substrate (RU5P) and metal ions
Analyse Structure of ribb complexed with substrate (RU5P) and metal ions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P8E
- Type
- protein
- Length
- 433 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
- Q9KKP2
- Ligands
- 5RP, ZN
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% 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 | 42% helix, 20% strand | Q9KKP2 |
| B | 3,4-dihydroxy-2-butanone 4-phosphate synthase (EC 4.1.99.12) | protein | 217 | 41% helix, 20% strand | Q9KKP2 |
Ligands and binding sites
- 5RP · Ribulose-5-phosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 10 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.67 | 0.92 | 30 | 5RP, ZN |
| 2 | 54 | 0.35 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1557 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4P8E · Structure of ribB complexed with substrate (Ru5P) and metal ions · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KKP2 · 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 Q9KKP2
- Elsewhere: RCSB PDB 4P8E · PDBe 4P8E · UniProt Q9KKP2
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