MolNFT v1 · #158188 · protein
Binary complex structure of the T130K mutant of ant-4'' with neomycin
6NMK · Kanamycin nucleotidyltransferase: “Binary complex structure of the T130K mutant of ant-4'' with neomycin”. X-ray diffraction, 3 ligands (NMY, MG, CA), 3 pockets (best druggability 0.79). MolNFT v1 #158188 on GenesisL1: 3D structure…
- PDB
- 6NMK
- Type
- protein
- Length
- 505 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kanamycin nucleotidyltransferase
- UniProt
- Q57514
- Ligands
- NMY, MG, CA
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kanamycin nucleotidyltransferase | protein | 252 | 58% helix, 14% strand | Q57514 |
| B | Kanamycin nucleotidyltransferase | protein | 253 | 58% helix, 14% strand | Q57514 |
Ligands and binding sites
- NMY · Neomycin · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
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 | 1129 | 0.79 | 0.81 | 126 | NMY, MG |
| 2 | 89 | 0.46 | 0.80 | 16 | empty |
| 3 | 61 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3035 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 6NMK · Binary complex structure of the T130K mutant of ANT-4'' with Neomycin · 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 6NMK · PDBe 6NMK · UniProt Q57514
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