Research workbench
Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase APH(4)-Ia, ternary complex with ADP and hygromycin B
Analyse Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W0O
- Type
- protein
- Length
- 295 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Escherichia coli
- Molecule
- Hygromycin-B 4-O-kinase
- EC
- 2.7.1.163
- UniProt
- P00557
- Ligands
- ADP, HY0
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · resolution 1.5 · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hygromycin-B 4-O-kinase (EC 2.7.1.163) | protein | 295 | 46% helix, 21% strand | P00557 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.67 | 0.76 | 74 | ADP, HY0 |
| 2 | 112 | 0.51 | 0.81 | 23 | empty |
| 3 | 59 | 0.30 | 0.74 | 12 | empty |
Compared structures
- 3W0O · Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- P00557 · AlphaFold monomer V2.0 prediction for hygromycin-B 4-O-kinase (P00557) · 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 P00557
- Elsewhere: RCSB PDB 3W0O · PDBe 3W0O · UniProt P00557
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