MolNFT v1 · #64703 · protein
Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoroadenine
3GB9: “Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoroadenine”. X-ray diffraction, 2 ligands (A2F, SO4), 7 pockets (best druggability 0.80). MolNFT v1 #64703 on GenesisL1: 3D structure, binding sites…
- PDB
- 3GB9
- Type
- protein
- Length
- 826 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
- A2F, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 283 | 36% helix, 23% strand | P00491 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 270 | 34% helix, 24% strand | P00491 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 273 | 34% helix, 24% strand | P00491 |
Ligands and binding sites
- A2F · 2-fluoroadenine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 33 copies · chains A, B, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.80 | 0.97 | 19 | empty |
| 2 | 475 | 0.70 | 0.81 | 61 | SO4 |
| 3 | 511 | 0.66 | 0.77 | 75 | A2F, SO4 |
| 4 | 266 | 0.59 | 0.79 | 49 | A2F, SO4 |
| 5 | 221 | 0.58 | 0.80 | 40 | A2F, SO4 |
Interfaces
3 interfaces between chains.
- B–C · 1176 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1150 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1132 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3GB9 · Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- P00491 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P00491) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 3GB9 · PDBe 3GB9 · UniProt P00491
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