MolNFT v1 · #82881 · protein
Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase APH(4)-ia, apo form
3W0M · Hygromycin-B 4-O-kinase: “Crystal structure of a thermostable mutant of aminoglycoside phosphotransferase APH(4)-ia, apo form”. X-ray diffraction, 3 pockets (best druggability 0.68). MolNFT v1 #82881 on GenesisL1: 3D structure…
- PDB
- 3W0M
- Type
- protein
- Length
- 293 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
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 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 | 293 | 46% helix, 21% strand | P00557 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 654 | 0.68 | 0.76 | 71 | MPD |
| 2 | 126 | 0.53 | 0.81 | 26 | empty |
| 3 | 59 | 0.37 | 0.80 | 12 | empty |
Compared structures
- 3W0M · 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 0.97
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 3W0M · PDBe 3W0M · UniProt P00557
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