Research workbench
Structure of uridylyltransferase mutant
Analyse Structure of uridylyltransferase mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K9Z
- Type
- protein
- Length
- 610 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.78
- Source
- Pyrobaculum aerophilum str. IM2
- Molecule
- Galactose-1-phosphate uridylyltransferase
- UniProt
- Q8ZXN7
- Ligands
- UDP, ZN, FE
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.78 · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactose-1-phosphate uridylyltransferase | protein | 309 | 31% helix, 23% strand | Q8ZXN7 |
| B | Galactose-1-phosphate uridylyltransferase | protein | 301 | 32% helix, 23% strand | Q8ZXN7 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- ACT · Acetate 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.72 | 0.82 | 41 | UDP |
| 2 | 512 | 0.69 | 0.79 | 47 | UDP |
| 3 | 459 | 0.68 | 0.79 | 62 | empty |
| 4 | 98 | 0.47 | 0.81 | 22 | empty |
| 5 | 94 | 0.47 | 0.81 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3147 Ų buried · 43 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6K9Z · Structure of uridylyltransferase mutant · 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 Q8ZXN7
- Elsewhere: RCSB PDB 6K9Z · PDBe 6K9Z · UniProt Q8ZXN7
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