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Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with 2-fluoro-2'-deoxyadenosine
Analyse Human purine nucleoside phosphorylase double mutant E201Q,N243D complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GGS
- Type
- protein
- Length
- 848 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
- 2FD, SO4
- Pockets
- 8 · best druggability 0.79
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 | 284 | 33% helix, 23% strand | P00491 |
| B | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 285 | 33% helix, 23% strand | P00491 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 279 | 34% helix, 24% strand | P00491 |
Ligands and binding sites
- 2FD · 5-(6-amino-2-fluoro-purin-9-yl)-2-hydroxymethyl-tetrahydro-furan-3-ol · ligand · 4 copies · chains A, C, B
- SO4 · Sulfate ion · ion · 30 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.79 | 0.97 | 19 | empty |
| 2 | 602 | 0.72 | 0.79 | 74 | 2FD, SO4 |
| 3 | 514 | 0.69 | 0.79 | 62 | 2FD, SO4 |
| 4 | 511 | 0.65 | 0.77 | 59 | SO4 |
| 5 | 357 | 0.63 | 0.78 | 60 | 2FD, SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1176 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1169 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1165 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3GGS · 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 C against A, TM-score 0.95
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 3GGS · PDBe 3GGS · UniProt P00491
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