Research workbench
Crystal structure of xylulokinase from chromobacterium violaceum
Analyse Crystal structure of xylulokinase from chromobacterium violaceum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HZ6
- Type
- protein
- Length
- 497 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylulokinase
- EC
- 2.7.1.17
- UniProt
- Q7NWW7
- Ligands
- ADP, XUL, PO4
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xylulokinase (EC 2.7.1.17) | protein | 497 | 40% helix, 21% strand | Q7NWW7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- XUL · D-xylulose · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 2 copies · chains A
- MLI · Malonate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.76 | 0.81 | 67 | GOL, XUL |
| 2 | 123 | 0.52 | 0.81 | 24 | ADP |
| 3 | 108 | 0.43 | 0.77 | 18 | empty |
| 4 | 140 | 0.42 | 0.75 | 18 | empty |
| 5 | 92 | 0.41 | 0.78 | 22 | empty |
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3HZ6 · Crystal structure of xylulokinase from Chromobacterium violaceum · 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 Q7NWW7
- Elsewhere: RCSB PDB 3HZ6 · PDBe 3HZ6 · UniProt Q7NWW7
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