Research workbench
UTP-bound UGPase from acinetobacter baumannii
Analyse UTP-bound UGPase from acinetobacter baumannii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KNJ
- Type
- protein
- Length
- 570 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.2
- Source
- Acinetobacter baumannii
- Molecule
- UTP--glucose-1-phosphate uridylyltransferase
- EC
- 2.7.7.9
- UniProt
- X2KZJ9
- Ligands
- UTP, SO4
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · resolution 3.2 · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 285 | 36% helix, 20% strand | X2KZJ9 |
| B | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 285 | 32% helix, 24% strand | X2KZJ9 |
Ligands and binding sites
- UTP · Uridine 5'-triphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
- GOL · Glycerol · additive · chains B
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 | 628 | 0.65 | 0.75 | 50 | SO4, UTP |
| 2 | 530 | 0.64 | 0.76 | 55 | UTP |
| 3 | 257 | 0.58 | 0.78 | 44 | empty |
| 4 | 150 | 0.48 | 0.77 | 22 | empty |
| 5 | 60 | 0.38 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2276 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6KNJ · UTP-bound ugpase from acinetobacter baumannii · 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 X2KZJ9
- Elsewhere: RCSB PDB 6KNJ · PDBe 6KNJ · UniProt X2KZJ9
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