› 6vt1

X-ray diffraction
2.38Å resolution

Naegleria gruberi RNA ligase D172A mutant apo

Released:
DOI: 10.2210/pdb6vt1/pdb
PDB entry 6vt1 coloured by chain, front view.
PDB entry 6vt1 coloured by chain, side view.
PDB entry 6vt1 coloured by chain, top view.
Source organism: Naegleria gruberi
Primary publication:
Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Unciuleac MC, Goldgur Y, Shuman S
OpenAccess logo Nucleic Acids Res 48 5603-5615 (2020)
PMID: 32315072

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112420 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
RNA ligase domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 340 amino acids
Theoretical weight: 38.62 KDa
Source organism: Naegleria gruberi
Expression system: Escherichia coli
UniProt:
  • Canonical: D2W2Z5 (Residues: 1-339; Coverage: 100%)
Gene name: NAEGRDRAFT_82186
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand AMP 4 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21212
Unit cell:
a: 125.271Å b: 104.183Å c: 120.556Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.233 0.232 0.276
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

Classification of domains in predicted structures of the human proteome.
Schaeffer et al. (2023)

1 mention without citation

Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Unciuleac et al. (2020)