MolNFT v1 · #92821 · protein
Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with phosphate
4GKA: “Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed…”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.78). MolNFT v1 #92821 on GenesisL1: 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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