MolNFT v1 · #92826 · protein
Crystal structure of the aminoglycoside phosphotransferase APH(3')-ia, with substrate kanamycin and small molecule inhibitor 1-na-PP1
4GKH · 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, 0J9, NA), 20 pockets (best druggability…
- PDB
- 4GKH
- Type
- protein
- Length
- 3,164 residues
- Chains
- 12
- 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, 0J9, NA, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 10 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 254 | 44% helix, 21% strand | B0VD92 |
| B | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 268 | 42% helix, 20% strand | B0VD92 |
| C | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 267 | 41% helix, 20% strand | B0VD92 |
| D | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 265 | 41% helix, 20% strand | B0VD92 |
| E | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 261 | 43% helix, 21% strand | B0VD92 |
| F | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 271 | 42% helix, 21% strand | B0VD92 |
| G, J | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 267 | 42% helix, 20% strand | B0VD92 |
| H | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 255 | 44% helix, 21% strand | B0VD92 |
| I | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 266 | 42% helix, 20% strand | B0VD92 |
| K | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 269 | 42% helix, 19% strand | B0VD92 |
Ligands and binding sites
- KAN · Kanamycin A · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 0J9 · 1-tert-butyl-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- NA · Sodium ion · metal · 14 copies · chains A, C, K, B, E, G, F, H, I, L
- CL · Chloride ion · ion · 2 copies · chains C, I
- ACT · Acetate ion · additive · 36 copies · chains A, B, C, D, I, E, F, G, H, J, K, L
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.80 | 0.82 | 93 | KAN, 0J9, ACT |
| 2 | 1110 | 0.80 | 0.81 | 88 | KAN, 0J9, ACT |
| 3 | 591 | 0.78 | 0.84 | 53 | KAN, 0J9, ACT |
| 4 | 375 | 0.78 | 0.88 | 45 | KAN |
| 5 | 258 | 0.77 | 0.90 | 43 | 0J9, ACT |
Interfaces
25 interfaces between chains.
- I–J · 2534 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2532 Ų buried · 35 hydrogen bonds · protein-protein
- E–F · 2308 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1942 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 1930 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 77 modified (engineered).
Compared structures
- 4GKH · 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 4GKH · PDBe 4GKH · UniProt B0VD92
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