Research workbench
Crystal structure of aminoglycoside phosphotransferase APH(2'')-iva ADP complex
Analyse Crystal structure of aminoglycoside phosphotransferase APH(2'')-iva ADP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N57
- Type
- protein
- Length
- 593 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APH(2'')-id
- UniProt
- O68183
- Ligands
- ADP, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | APH(2'')-id | protein | 296 | 48% helix, 16% strand | O68183 |
| B | APH(2'')-id | protein | 297 | 46% helix, 15% strand | O68183 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1128 | 0.77 | 0.79 | 80 | MG, ADP |
| 2 | 929 | 0.73 | 0.77 | 77 | MG, ADP |
| 3 | 738 | 0.69 | 0.76 | 61 | empty |
| 4 | 85 | 0.39 | 0.77 | 14 | empty |
| 5 | 84 | 0.34 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 247 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4N57 · Crystal structure of aminoglycoside phosphotransferase APH(2'')-IVa ADP 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 4N57 · PDBe 4N57 · UniProt O68183
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