MolNFT v1 · #136026 · protein
Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with dadme-immg and phosphate
5UGF: “Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with dadme-immg and…”. X-ray diffraction, 2 ligands (IM5, PO4), 20 pockets (best druggability 0.80). MolNFT v1 #136026 on GenesisL1: 3D structure…
- PDB
- 5UGF
- Type
- protein
- Length
- 1,721 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- P00491
- Ligands
- IM5, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 286 | 34% helix, 23% strand | P00491 |
| B, E, F | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 287 | 34% helix, 23% strand | P00491 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 288 | 34% helix, 23% strand | P00491 |
Ligands and binding sites
- IM5 · 2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one · ligand · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 29 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.80 | 0.98 | 28 | PO4, IM5 |
| 2 | 125 | 0.80 | 0.98 | 30 | PO4, IM5 |
| 3 | 129 | 0.80 | 0.97 | 31 | PO4, IM5 |
| 4 | 115 | 0.79 | 0.98 | 24 | PO4, IM5 |
| 5 | 122 | 0.78 | 0.97 | 30 | PO4, IM5 |
Interfaces
7 interfaces between chains.
- B–C · 1491 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1444 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1442 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1414 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 1383 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5UGF · Crystal structure of human purine nucleoside phosphorylase (F159Y) mutant complexed with… · 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 P00491
- Elsewhere: RCSB PDB 5UGF · PDBe 5UGF · UniProt P00491
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