MolNFT v1 · #91491 · protein
Crystal structure of the aminoglycoside phosphotransferase APH(3')-ia, with substrate kanamycin and small molecule inhibitor pyrazolopyrimidine PP1
4FEV · Aminoglycoside 3'-phosphotransferase APHA1-iab: “Crystal structure of the aminoglycoside phosphotransferase APH(3')-ia, with substrate kanamycin and small…”. X-ray diffraction, 3 ligands (KAN, PP1, NA), 15 pockets (best druggability…
- PDB
- 4FEV
- 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, PP1, NA
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 263 | 40% helix, 19% strand | B0VD92 |
| B | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 254 | 43% helix, 21% strand | B0VD92 |
| C | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 254 | 45% helix, 21% strand | B0VD92 |
| D | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 271 | 41% helix, 21% strand | B0VD92 |
| E | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 268 | 41% helix, 21% strand | B0VD92 |
| F | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 252 | 43% helix, 19% strand | B0VD92 |
Ligands and binding sites
- KAN · Kanamycin A · ligand · 6 copies · chains A, D, B, C, E, F
- PP1 · 1-ter-butyl-3-P-tolyl-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
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.84 | 0.86 | 97 | KAN, PP1 |
| 2 | 831 | 0.84 | 0.86 | 93 | KAN, PP1 |
| 3 | 581 | 0.80 | 0.85 | 74 | KAN, PP1 |
| 4 | 749 | 0.71 | 0.77 | 76 | KAN, PP1 |
| 5 | 652 | 0.68 | 0.76 | 61 | PP1 |
Interfaces
7 interfaces between chains.
- A–B · 2130 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1936 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 1210 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 811 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 446 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4FEV · 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 4FEV · PDBe 4FEV · UniProt B0VD92
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