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The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation
Analyse The crystal structure of pyrimidine nucleoside phosphorylase in a closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BRW
- Type
- protein
- Length
- 866 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (pyrimidine nucleoside phosphorylase)
- EC
- 2.4.2.2
- UniProt
- P77836
- Ligands
- URA, CA, PO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (pyrimidine nucleoside phosphorylase) (EC 2.4.2.2) | protein | 433 | 46% helix, 16% strand | P77836 |
Ligands and binding sites
- URA · Uracil · ligand · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.76 | 0.98 | 27 | PO4, URA |
| 2 | 803 | 0.75 | 0.80 | 65 | PO4 |
| 3 | 482 | 0.65 | 0.77 | 69 | empty |
| 4 | 86 | 0.53 | 0.85 | 19 | empty |
| 5 | 100 | 0.47 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1098 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1BRW · The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation · the same entry in another collection · chain A against A, TM-score 1.00
- P77836 · AlphaFold monomer V2.0 prediction for pyrimidine-nucleoside phosphorylase (P77836) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P77836
- Elsewhere: RCSB PDB 1BRW · PDBe 1BRW · UniProt P77836
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