Research workbench
Crystal structure of streptococcus pyogenes uridine phosphorylase reveals a subclass of the np-I superfamily
Analyse Crystal structure of streptococcus pyogenes uridine phosphorylase reveals a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QPB
- Type
- protein
- Length
- 4,487 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uridine phosphorylase
- EC
- 2.4.2.3
- UniProt
- Q5XA29
- Ligands
- R1P, URA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 36% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, H, I | Uridine phosphorylase (EC 2.4.2.3) | protein | 250 | 37% helix, 29% strand | Q5XA29 |
| C | Uridine phosphorylase (EC 2.4.2.3) | protein | 254 | 36% helix, 28% strand | Q5XA29 |
| D, E, K, M | Uridine phosphorylase (EC 2.4.2.3) | protein | 249 | 35% helix, 29% strand | Q5XA29 |
| F | Uridine phosphorylase (EC 2.4.2.3) | protein | 251 | 37% helix, 29% strand | Q5XA29 |
| G, L, N, O | Uridine phosphorylase (EC 2.4.2.3) | protein | 249 | 36% helix, 29% strand | Q5XA29 |
| J, P, Q | Uridine phosphorylase (EC 2.4.2.3) | protein | 248 | 36% helix, 29% strand | Q5XA29 |
| R | Uridine phosphorylase (EC 2.4.2.3) | protein | 246 | 37% helix, 29% strand | Q5XA29 |
Ligands and binding sites
- R1P · 1-O-phosphono-alpha-D-ribofuranose · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
- URA · Uracil · ligand · 18 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
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 | 1189 | 0.80 | 0.81 | 98 | empty |
| 2 | 1166 | 0.79 | 0.81 | 100 | empty |
| 3 | 1158 | 0.79 | 0.81 | 101 | empty |
| 4 | 940 | 0.77 | 0.80 | 89 | empty |
| 5 | 84 | 0.74 | 0.97 | 25 | R1P, URA |
Interfaces
41 interfaces between chains.
- C–D · 2057 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 1911 Ų buried · 27 hydrogen bonds · protein-protein
- O–P · 1890 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1890 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1886 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3QPB · Crystal Structure of Streptococcus Pyogenes Uridine Phosphorylase Reveals a Subclass of… · the same entry in another collection · chain B against B, 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 Q5XA29
- Elsewhere: RCSB PDB 3QPB · PDBe 3QPB · UniProt Q5XA29
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