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Crystal structure of the aminoglycoside phosphotransferase APH(3')-ia, with substrate kanamycin and small molecule inhibitor 1-nm-PP1
Analyse Crystal structure of the aminoglycoside phosphotransferase APH(3')-ia, with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GKI
- Type
- protein
- Length
- 3,171 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, 0JN, NA, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G, J | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 272 | 42% helix, 20% strand | B0VD92 |
| B | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 257 | 43% helix, 21% strand | B0VD92 |
| D, I | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 254 | 43% helix, 20% strand | B0VD92 |
| E | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 266 | 42% helix, 20% strand | B0VD92 |
| F | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 261 | 42% helix, 21% strand | B0VD92 |
| H | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 255 | 44% helix, 20% strand | B0VD92 |
| K | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 271 | 40% helix, 21% strand | B0VD92 |
| L | Aminoglycoside 3'-phosphotransferase APHA1-iab (EC 2.7.1.95) | protein | 265 | 41% helix, 20% 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
- 0JN · 1-tert-butyl-3-(naphthalen-1-ylmethyl)-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, D, E, F, G, H, J, K, L
- CL · Chloride ion · ion · chains A
- ACT · Acetate ion · additive · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, I, J
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 | 957 | 0.81 | 0.83 | 86 | KAN, 0JN |
| 2 | 925 | 0.80 | 0.82 | 95 | KAN, 0JN, NA |
| 3 | 1049 | 0.80 | 0.82 | 86 | KAN, 0JN |
| 4 | 536 | 0.78 | 0.85 | 51 | KAN, 0JN |
| 5 | 674 | 0.78 | 0.83 | 63 | KAN, 0JN |
Interfaces
22 interfaces between chains.
- K–L · 2482 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 2399 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2109 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2013 Ų buried · 26 hydrogen bonds · protein-protein
- I–J · 2003 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 77 modified (engineered).
Compared structures
- 4GKI · 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 4GKI · PDBe 4GKI · UniProt B0VD92
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