Research workbench
The crystal structure of xylulose kinase from rhodospirillum rubrum
Analyse The crystal structure of xylulose kinase from rhodospirillum rubrum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IFR
- Type
- protein
- Length
- 968 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carbohydrate kinase, fggy
- EC
- 2.7.1.17
- UniProt
- Q2RUX7
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carbohydrate kinase, fggy (EC 2.7.1.17) | protein | 488 | 42% helix, 22% strand | Q2RUX7 |
| B | Carbohydrate kinase, fggy (EC 2.7.1.17) | protein | 480 | 43% helix, 20% strand | Q2RUX7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.75 | 0.78 | 100 | PO4 |
| 2 | 609 | 0.64 | 0.75 | 57 | empty |
| 3 | 185 | 0.51 | 0.77 | 29 | empty |
| 4 | 58 | 0.35 | 0.78 | 16 | empty |
| 5 | 51 | 0.31 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 106 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3IFR · The crystal structure of xylulose kinase from Rhodospirillum rubrum · 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 Q2RUX7
- Elsewhere: RCSB PDB 3IFR · PDBe 3IFR · UniProt Q2RUX7
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