Research workbench
Crystal structure of aminoglycoside phosphotransferase APH(2")- ID/APH(2")-iva in complex with kanamycin
Analyse Crystal structure of aminoglycoside phosphotransferase APH(2")- ID/APH(2")-iva… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DFB
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APH(2")-id
- UniProt
- O68183
- Ligands
- KAN, CL
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | APH(2")-id | protein | 297 | 46% helix, 15% strand | O68183 |
| B | APH(2")-id | protein | 301 | 48% helix, 15% strand | O68183 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.83 | 0.86 | 91 | empty |
| 2 | 190 | 0.66 | 0.85 | 28 | empty |
| 3 | 160 | 0.64 | 0.85 | 30 | empty |
| 4 | 227 | 0.55 | 0.77 | 27 | empty |
| 5 | 80 | 0.54 | 0.86 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1278 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4DFB · Crystal structure of aminoglycoside phosphotransferase aph(2")-id/aph(2")-iva in complex… · 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 O68183
- Elsewhere: RCSB PDB 4DFB · PDBe 4DFB · UniProt O68183
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