MolNFT v1 · #154828 · protein
Uridine and triphosphate-bound ugpase from acinetobacter baumannii
6KNL · UTP--glucose-1-phosphate uridylyltransferase: “Uridine and triphosphate-bound ugpase from acinetobacter baumannii”. X-ray diffraction, 3 ligands (URI, 3PO, SO4), 7 pockets (best druggability 0.71). MolNFT v1 #154828 on GenesisL1: 3D…
- PDB
- 6KNL
- Type
- protein
- Length
- 580 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UTP--glucose-1-phosphate uridylyltransferase
- EC
- 2.7.7.9
- UniProt
- X2KZJ9
- Ligands
- URI, 3PO, SO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) | protein | 290 | 36% helix, 22% strand | X2KZJ9 |
Ligands and binding sites
- URI · Uridine · ligand · 2 copies · chains A, B
- 3PO · Triphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 820 | 0.71 | 0.76 | 62 | URI, 3PO |
| 2 | 697 | 0.69 | 0.77 | 52 | URI, 3PO |
| 3 | 130 | 0.49 | 0.79 | 30 | empty |
| 4 | 167 | 0.49 | 0.77 | 21 | empty |
| 5 | 127 | 0.46 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2399 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6KNL · Uridine and triphosphate-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 6KNL · PDBe 6KNL · UniProt X2KZJ9
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