Research workbench
Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with dadme-immg and phosphate
Analyse Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EAR
- Type
- protein
- Length
- 855 residues
- Chains
- 3
- 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
- 5 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 283 | 34% helix, 24% strand | P00491 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 287 | 33% helix, 23% strand | P00491 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 285 | 32% 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 · 3 copies · chains A, C, B
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.80 | 0.97 | 33 | IM5, PO4 |
| 2 | 127 | 0.79 | 0.97 | 26 | IM5, PO4 |
| 3 | 126 | 0.79 | 0.96 | 27 | IM5, PO4 |
| 4 | 95 | 0.78 | 0.98 | 15 | empty |
| 5 | 458 | 0.62 | 0.76 | 64 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1382 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1379 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 1363 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nonstandard).
Compared structures
- 4EAR · Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant… · 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 4EAR · PDBe 4EAR · UniProt P00491
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