Research workbench
Crystal structure of aminoglycoside 7"-phoshotransferase-ia (APH(7")- IA/HYG) from streptomyces hygroscopicus complexed with hygromycin B
Analyse Crystal structure of aminoglycoside 7"-phoshotransferase-ia (APH(7")- IA/HYG)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IY9
- Type
- protein
- Length
- 649 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hygromycin-B 7''-O-kinase
- EC
- 2.7.1.119
- UniProt
- P09979
- Ligands
- HY0
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hygromycin-B 7''-O-kinase (EC 2.7.1.119) | protein | 325 | 45% helix, 12% strand | P09979 |
| B | Hygromycin-B 7''-O-kinase (EC 2.7.1.119) | protein | 324 | 43% helix, 12% strand | P09979 |
Ligands and binding sites
- HY0 · Hygromycin B variant · ligand · 2 copies · chains A, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 2 copies · chains A, B
- FLC · Citrate anion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 334 | 0.72 | 0.85 | 49 | FLC |
| 2 | 484 | 0.68 | 0.79 | 51 | HY0, NHE |
| 3 | 188 | 0.67 | 0.86 | 25 | empty |
| 4 | 333 | 0.67 | 0.81 | 52 | HY0 |
| 5 | 130 | 0.50 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 844 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 6IY9 · Crystal structure of aminoglycoside 7"-phoshotransferase-Ia (APH(7")-Ia/HYG) from… · the same entry in another collection · chain A against A, TM-score 1.00
- P09979 · AlphaFold monomer V2.0 prediction for hygromycin-B 7''-O-kinase (P09979) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P09979
- Elsewhere: RCSB PDB 6IY9 · PDBe 6IY9 · UniProt P09979
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