Research workbench
Ternary structure of the T130K mutant of ant-4'' with neomycin and ampcpp
Analyse Ternary structure of the T130K mutant of ant-4'' with neomycin and ampcpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NML
- 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, APC, MG
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Kanamycin nucleotidyltransferase | protein | 253 | 57% helix, 14% strand | Q57514 |
| B | Kanamycin nucleotidyltransferase | protein | 252 | 58% helix, 14% strand | Q57514 |
Ligands and binding sites
- NMY · Neomycin · ligand · 2 copies · chains A, B
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, B
- MG · Magnesium 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.78 | 0.80 | 119 | NMY, APC, MG |
| 2 | 106 | 0.47 | 0.79 | 17 | empty |
| 3 | 68 | 0.29 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3027 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 6NML · Ternary structure of the T130K mutant of ANT-4'' with Neomycin and AMPCPP · the same entry in another collection · chain B against B, 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 6NML · PDBe 6NML · UniProt Q57514
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