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Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with 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
- 4GKA
- Type
- protein
- Length
- 1,608 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
- PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 271 | 32% helix, 25% strand | P00491 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 269 | 33% helix, 25% strand | P00491 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 266 | 34% helix, 25% strand | P00491 |
| D | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 268 | 34% helix, 25% strand | P00491 |
| E | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 267 | 33% helix, 25% strand | P00491 |
| F | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 267 | 34% helix, 25% strand | P00491 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 2 copies · chains A, C, F
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 | 95 | 0.78 | 0.98 | 17 | empty |
| 2 | 83 | 0.76 | 0.97 | 15 | empty |
| 3 | 356 | 0.60 | 0.77 | 64 | empty |
| 4 | 340 | 0.59 | 0.77 | 53 | empty |
| 5 | 194 | 0.57 | 0.80 | 31 | PO4 |
Interfaces
7 interfaces between chains.
- A–C · 1203 Ų buried · 15 hydrogen bonds · protein-protein
- D–F · 1152 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1152 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1137 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1132 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4GKA · 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 4GKA · PDBe 4GKA · UniProt P00491
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