MolNFT v1 · #91492 · protein
Crystal structure of the aminoglycoside phosphotransferase APH(3')-ia, with substrate kanamycin and small molecule inhibitor pyrazolopyrimidine PP2
4FEW · Aminoglycoside 3'-phosphotransferase APHA1-iab: “Crystal structure of the aminoglycoside phosphotransferase APH(3')-ia, with substrate kanamycin and small…”. X-ray diffraction, 4 ligands (KAN, PP2, NA), 20 pockets (best druggability…
- PDB
- 4FEW
- Type
- protein
- Length
- 1,562 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside 3'-phosphotransferase APHA1-iab
- EC
- 2.7.1.95
- UniProt
- B0VD92
- Ligands
- KAN, PP2, NA, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 266 | 41% helix, 20% strand | B0VD92 |
| B | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 256 | 43% helix, 21% strand | B0VD92 |
| C, E | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 254 | 43% helix, 21% strand | B0VD92 |
| D | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 266 | 39% helix, 21% strand | B0VD92 |
| F | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 266 | 41% helix, 21% strand | B0VD92 |
Ligands and binding sites
- KAN · Kanamycin A · ligand · 6 copies · chains A, D, B, C, E, F
- PP2 · 1-tert-butyl-3-(4-chloro-phenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-ylamine · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 7 copies · chains A, B, D, E, F
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 6 copies · chains A, B, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.85 | 0.86 | 109 | KAN, PP2 |
| 2 | 685 | 0.82 | 0.87 | 66 | KAN, PP2 |
| 3 | 574 | 0.72 | 0.80 | 51 | KAN, PP2 |
| 4 | 787 | 0.72 | 0.77 | 74 | KAN, PP2 |
| 5 | 836 | 0.71 | 0.77 | 78 | KAN, PP2 |
Interfaces
8 interfaces between chains.
- A–B · 2143 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 1802 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1796 Ų buried · 27 hydrogen bonds · protein-protein
- C–E · 522 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 486 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 38 modified (engineered).
Compared structures
- 4FEW · Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate… · 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 B0VD92
- Elsewhere: RCSB PDB 4FEW · PDBe 4FEW · UniProt B0VD92
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.