MolNFT v1 · #159756 · protein
Ternary structure of the E52D mutant of ant-4 with neomycin and ampcpp
6P06 · Kanamycin nucleotidyltransferase: “Ternary structure of the E52D mutant of ant-4 with neomycin and ampcpp”. X-ray diffraction, 3 ligands (NMY, APC, CA), 3 pockets (best druggability 0.80). MolNFT v1 #159756 on GenesisL1: 3D…
- PDB
- 6P06
- Type
- protein
- Length
- 505 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kanamycin nucleotidyltransferase
- EC
- 2.7.7.-
- UniProt
- P05058
- Ligands
- NMY, APC, CA
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kanamycin nucleotidyltransferase (EC 2.7.7.-) | protein | 253 | 57% helix, 14% strand | P05058 |
| B | Kanamycin nucleotidyltransferase (EC 2.7.7.-) | protein | 252 | 58% helix, 14% strand | P05058 |
Ligands and binding sites
- NMY · Neomycin · ligand · 2 copies · chains A, B
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.80 | 0.83 | 108 | APC, CA |
| 2 | 109 | 0.52 | 0.82 | 18 | empty |
| 3 | 65 | 0.29 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3001 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 6P06 · Ternary structure of the E52D mutant of ANT-4 with Neomycin and AMPCPP · the same entry in another collection · chain A against A, TM-score 1.00
- P05058 · AlphaFold monomer V2.0 prediction for kanamycin nucleotidyltransferase (P05058) · a predicted model of the same protein · 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 P05058
- Elsewhere: RCSB PDB 6P06 · PDBe 6P06 · UniProt P05058
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