MolNFT v2 · #15719 · protein
Crystal structure of aminoglycoside-3'-phosphotransferase-IIa
1ND4 · Aminoglycoside 3'-phosphotransferase: “Crystal structure of aminoglycoside-3'-phosphotransferase-IIa”. X-ray diffraction at 2.1, 3 ligands (KAN, MG, NA), 3 pockets (best druggability 0.66). MolNFT v2 #15719 on GenesisL1: 3D…
- PDB
- 1ND4
- Type
- protein
- Length
- 510 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Klebsiella pneumoniae
- 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 · resolution 2.1 · 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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