Research workbench
Crystal structure of 3',5"-aminoglycoside phosphotransferase type iiia amppnp butirosin a complex
Analyse Crystal structure of 3',5"-aminoglycoside phosphotransferase type iiia amppnp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TM0
- Type
- protein
- Length
- 263 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminoglycoside 3'-phosphotransferase
- EC
- 2.7.1.95
- UniProt
- P0A3Y5
- Ligands
- ANP, B31, MG
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminoglycoside 3'-phosphotransferase (EC 2.7.1.95) | protein | 263 | 41% helix, 19% strand | P0A3Y5 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- B31 · (2S)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,6-dideoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxy-3-(beta-D-xylofuranosyloxy)cyclohexyl]-2-hydroxybutanamide · 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.68 | 0.79 | 53 | ANP, B31, MG |
| 2 | 67 | 0.30 | 0.73 | 14 | empty |
Compared structures
- 3TM0 · Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa AMPPNP Butirosin A… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A3Y5 · AlphaFold monomer V2.0 prediction for aminoglycoside 3'-phosphotransferase (P0A3Y5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P0A3Y5
- Elsewhere: RCSB PDB 3TM0 · PDBe 3TM0 · UniProt P0A3Y5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.