› 6p08

X-ray diffraction
2.27Å resolution

Ternary structure of the E52D mutant of ANT-4'' with Neomycin, AMP and Pyrophosphate

Released:
DOI: 10.2210/pdb6p08/pdb
PDB entry 6p08 coloured by chain, front view.
PDB entry 6p08 coloured by chain, side view.
PDB entry 6p08 coloured by chain, top view.
Source organism: Bacillus sp. (in: Bacteria)
Primary publication:
"Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer Reaction
Selvaraj B, Kocaman S, Trifas M, Serpersu EH, Cuneo MJ
ACS Catalysis 10 3548-3555 (2020)

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138346 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Kanamycin nucleotidyltransferase Chains: A, D
Molecule details ›
Chains: A, D
Length: 256 amino acids
Theoretical weight: 29.12 KDa
Source organism: Bacillus sp. (in: Bacteria)
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
UniProt:
  • Canonical: P05058 (Residues: 1-253; Coverage: 100%)
Gene names: kan, knt
Sequence domains: KNTase C-terminal domain

Ligands and Environments

4 bound ligands:
Ligand NMY 2 x NMY
Ligand PPV 2 x PPV
Ligand MG 4 x MG
Ligand AMP 2 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 59.75Å b: 99.3Å c: 101.49Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.225
Expression system: Escherichia coli-Pichia pastoris shuttle vector pPpARG4

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