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The crystal structure of xylulose kinase from bifidobacterium adolescentis
Analyse The crystal structure of xylulose kinase from bifidobacterium adolescentis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I8B
- Type
- protein
- Length
- 506 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylulose kinase
- UniProt
- A1A0I0
- Ligands
- MG
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylulose kinase | protein | 506 | 37% helix, 20% strand | A1A0I0 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.68 | 0.76 | 58 | empty |
| 2 | 90 | 0.54 | 0.84 | 24 | empty |
| 3 | 60 | 0.30 | 0.74 | 12 | empty |
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3I8B · The crystal structure of xylulose kinase from Bifidobacterium adolescentis · 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 A1A0I0
- Elsewhere: RCSB PDB 3I8B · PDBe 3I8B · UniProt A1A0I0
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