Research workbench
Crystal structure of aminoglycoside-3'-phosphotransferase- iia
Analyse Crystal structure of aminoglycoside-3'-phosphotransferase- iia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ND4
- Type
- protein
- Length
- 510 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
- P00552
- Ligands
- KAN, MG, NA
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminoglycoside 3'-phosphotransferase (EC 2.7.1.95) | protein | 255 | 40% helix, 19% strand | P00552 |
Ligands and binding sites
- KAN · Kanamycin A · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
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 | 574 | 0.66 | 0.76 | 53 | MG, ACT, NA, KAN |
| 2 | 389 | 0.64 | 0.78 | 39 | empty |
| 3 | 482 | 0.63 | 0.76 | 48 | ACT, NA, KAN |
Interfaces
1 interface between chains.
- A–B · 311 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1ND4 · Crystal structure of aminoglycoside-3'-phosphotransferase-IIa · the same entry in another collection · chain A against A, TM-score 1.00
- P00552 · AlphaFold monomer V2.0 prediction for aminoglycoside 3'-phosphotransferase (P00552) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P00552
- Elsewhere: RCSB PDB 1ND4 · PDBe 1ND4 · UniProt P00552
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