Research workbench
Crystal structure of APH(2")-iva in complex with plazomicin
Analyse Crystal structure of APH(2")-iva in complex with plazomicin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CD7
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APH(2'')-id
- UniProt
- O68183
- Ligands
- EDS, CL
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | APH(2'')-id | protein | 299 | 49% helix, 15% strand | O68183 |
| B | APH(2'')-id | protein | 298 | 48% helix, 15% strand | O68183 |
Ligands and binding sites
- EDS · (2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-{[(2-hydroxyethyl)amino]methyl}-3,4-dihydro-2H-pyran-2-yl]oxy}-2-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide · ligand · chains B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.77 | 0.86 | 57 | empty |
| 2 | 209 | 0.66 | 0.84 | 30 | empty |
| 3 | 215 | 0.64 | 0.83 | 31 | empty |
| 4 | 66 | 0.62 | 0.91 | 16 | empty |
| 5 | 93 | 0.55 | 0.85 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1286 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 6CD7 · Crystal structure of APH(2)-IVa in complex with plazomicin" · 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 6CD7 · PDBe 6CD7 · UniProt O68183
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