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Ternary complex structure of the T130K mutant of ant-4'' with neomycin and ATP (no pyrophosphate)
Analyse Ternary complex structure of the T130K mutant of ant-4'' with neomycin and ATP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NMN
- Type
- protein
- Length
- 506 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kanamycin nucleotidyltransferase
- UniProt
- Q57514
- Ligands
- NMY, A, MG
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 55% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kanamycin nucleotidyltransferase | protein | 253 | 55% helix, 13% strand | Q57514 |
Ligands and binding sites
- NMY · Neomycin · ligand · 2 copies · chains A, B
- A · Adenosine-5'-monophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.80 | 0.81 | 138 | NMY, A, MG |
| 2 | 68 | 0.32 | 0.75 | 15 | empty |
| 3 | 60 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3133 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 6NMN · Ternary complex structure of the T130K mutant of ANT-4'' with Neomycin and ATP (No… · 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 Q57514
- Elsewhere: RCSB PDB 6NMN · PDBe 6NMN · UniProt Q57514
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