MolNFT v1 · #168656 · protein
2.70 ångström resolution crystal structure of uracil phosphoribosyl transferase from klebsiella pneumoniae
6WN8 · Uracil phosphoribosyltransferase: “2.70 ångström resolution crystal structure of uracil phosphoribosyl transferase from klebsiella pneumoniae”. X-ray diffraction, 5 ligands (BDF, GLC, FRU), 20 pockets (best druggability 0.85).…
- PDB
- 6WN8
- Type
- protein
- Length
- 2,087 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil phosphoribosyltransferase
- EC
- 2.4.2.9
- UniProt
- A0A1Y0PUH0
- Ligands
- BDF, GLC, FRU, SO4, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, G, H | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 209 | 33% helix, 31% strand | A0A1Y0PUH0 |
| B | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 206 | 34% helix, 32% strand | A0A1Y0PUH0 |
| C, E, I, J | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 210 | 32% helix, 31% strand | A0A1Y0PUH0 |
| D | Uracil phosphoribosyltransferase (EC 2.4.2.9) | protein | 205 | 34% helix, 31% strand | A0A1Y0PUH0 |
Ligands and binding sites
- BDF · beta-D-fructopyranose · ligand · 5 copies · chains A, B, C, E, F, H
- GLC · alpha-D-glucopyranose · sugar · chains E, F
- FRU · beta-D-fructofuranose · sugar · chains E, F
- SO4 · Sulfate ion · ion · 91 copies · chains A, D, B, C, E, F, H, G, I, J
- CL · Chloride ion · ion · 23 copies · chains A, B, C, D, E, F, G, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.85 | 0.87 | 101 | SO4 |
| 2 | 782 | 0.84 | 0.87 | 92 | SO4 |
| 3 | 892 | 0.83 | 0.85 | 80 | SO4 |
| 4 | 210 | 0.76 | 0.91 | 31 | SO4 |
| 5 | 213 | 0.75 | 0.90 | 29 | SO4 |
Interfaces
19 interfaces between chains.
- I–J · 1954 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 1926 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1891 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1876 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1829 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6WN8 · 2.70 Angstrom Resolution Crystal Structure of Uracil Phosphoribosyl Transferase from… · 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 A0A1Y0PUH0
- Elsewhere: RCSB PDB 6WN8 · PDBe 6WN8 · UniProt A0A1Y0PUH0
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