MolNFT v1 · #89570 · protein
Crystal structure of aminoglycoside-2''-phosphotransferase type iva in complex with adenosine
4DT8 · APH(2'')-id: “Crystal structure of aminoglycoside-2''-phosphotransferase type iva in complex with adenosine”. X-ray diffraction, 2 ligands (ADN, CL), 10 pockets (best druggability 0.71). MolNFT v1 #89570 on GenesisL1: 3D structure…
- PDB
- 4DT8
- Type
- protein
- Length
- 597 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- APH(2'')-id
- UniProt
- O68183
- Ligands
- ADN, CL
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | APH(2'')-id | protein | 301 | 48% helix, 15% strand | O68183 |
| B | APH(2'')-id | protein | 296 | 48% helix, 15% strand | O68183 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 280 | 0.71 | 0.85 | 36 | empty |
| 2 | 147 | 0.67 | 0.88 | 29 | empty |
| 3 | 146 | 0.67 | 0.88 | 27 | ADN |
| 4 | 222 | 0.66 | 0.84 | 35 | ADN |
| 5 | 51 | 0.52 | 0.89 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1181 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 4DT8 · Crystal Structure of Aminoglycoside-2''-Phosphotransferase Type IVa in Complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 O68183
- Elsewhere: RCSB PDB 4DT8 · PDBe 4DT8 · UniProt O68183
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