MolNFT v1 · #82887 · protein
Crystal structure of aminoglycoside phosphotransferase APH(4)-ia, ternary complex with AMP-pnp and hygromycin B
3W0S · Hygromycin-B 4-O-kinase: “Crystal structure of aminoglycoside phosphotransferase APH(4)-ia, ternary complex with AMP-pnp and hygromycin…”. X-ray diffraction, 3 ligands (HY0, ANP, MG), 3 pockets (best druggability 0.57). MolNFT v1…
- PDB
- 3W0S
- Type
- protein
- Length
- 298 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hygromycin-B 4-O-kinase
- EC
- 2.7.1.163
- UniProt
- P00557
- Ligands
- HY0, ANP, MG
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hygromycin-B 4-O-kinase (EC 2.7.1.163) | protein | 298 | 47% helix, 21% strand | P00557 |
Ligands and binding sites
- HY0 · Hygromycin B variant · ligand · chains A
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.57 | 0.76 | 40 | HY0, MG |
| 2 | 275 | 0.56 | 0.77 | 38 | ANP |
| 3 | 75 | 0.52 | 0.85 | 21 | empty |
Compared structures
- 3W0S · Crystal structure of aminoglycoside phosphotransferase APH(4)-Ia, ternary complex with… · 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 3W0S · PDBe 3W0S · UniProt P00557
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