Research workbench
Crystal structure of 3',5"-aminoglycoside phosphotransferase type iiia amppnp 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
- 1J7U
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- 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, MG
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminoglycoside 3'-phosphotransferase (EC 2.7.1.95) | protein | 263 | 39% helix, 19% strand | P0A3Y5 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.82 | 0.86 | 79 | MG, ANP |
| 2 | 304 | 0.72 | 0.86 | 39 | MG, ANP |
| 3 | 170 | 0.63 | 0.85 | 29 | empty |
| 4 | 57 | 0.49 | 0.86 | 16 | empty |
| 5 | 56 | 0.38 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1527 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1J7U · Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa AMPPNP Complex · 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 1J7U · PDBe 1J7U · UniProt P0A3Y5
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