MolNFT v1 · #159758 · protein
Ternary structure of the E52D mutant of ant-4'' with neomycin, AMP and pyrophosphate
6P08 · Kanamycin nucleotidyltransferase: “Ternary structure of the E52D mutant of ant-4'' with neomycin, AMP and pyrophosphate”. X-ray diffraction, 4 ligands (NMY, PPV, AMP), 4 pockets (best druggability 0.78). MolNFT v1 #159758 on…
- PDB
- 6P08
- Type
- protein
- Length
- 504 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, PPV, AMP, MG
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Kanamycin nucleotidyltransferase (EC 2.7.7.-) | protein | 252 | 57% helix, 14% strand | P05058 |
Ligands and binding sites
- NMY · Neomycin · ligand · 2 copies · chains A, D
- PPV · Pyrophosphate · ligand · 2 copies · chains A, D
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.78 | 0.80 | 124 | NMY, PPV, MG, AMP |
| 2 | 123 | 0.51 | 0.80 | 18 | empty |
| 3 | 73 | 0.46 | 0.82 | 15 | empty |
| 4 | 60 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–D · 2981 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 6P08 · Ternary structure of the E52D mutant of ANT-4'' with Neomycin, AMP and Pyrophosphate · 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 0.99
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 6P08 · PDBe 6P08 · UniProt P05058
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