MolNFT v1 · #12667 · protein
Kanamycin nucleotidyltransferase
1KNY: “Kanamycin nucleotidyltransferase”. X-ray diffraction, 3 ligands (APC, KAN, MG), 2 pockets (best druggability 0.79). MolNFT v1 #12667 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KNY
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kanamycin nucleotidyltransferase
- EC
- 2.7.7.-
- UniProt
- P05057
- Ligands
- APC, KAN, MG
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 56% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kanamycin nucleotidyltransferase (EC 2.7.7.-) | protein | 253 | 56% helix, 14% strand | P05057 |
Ligands and binding sites
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- KAN · Kanamycin A · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
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 | 1023 | 0.79 | 0.81 | 108 | APC, KAN, MG |
| 2 | 87 | 0.32 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 3030 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
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 P05057
- Elsewhere: RCSB PDB 1KNY · PDBe 1KNY · UniProt P05057
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