› 5epm

X-ray diffraction
1.75Å resolution

Ceratotoxin variant in complex with specific antibody Fab fragment

Released:
DOI: 10.2210/pdb5epm/pdb
PDB entry 5epm coloured by chain, front view.
PDB entry 5epm coloured by chain, side view.
PDB entry 5epm coloured by chain, top view.
Source organisms:
Primary publication:
Engineering Highly Potent and Selective Microproteins against Nav1.7 Sodium Channel for Treatment of Pain.
Shcherbatko A, Rossi A, Foletti D, Zhu G, Bogin O, Galindo Casas M, Rickert M, Hasa-Moreno A, Bartsevich V, Crameri A, Steiner AR, Henningsen R, Gill A, Pons J, Shelton DL, Rajpal A, Strop P
J Biol Chem 291 13974-13986 (2016)
PMID: 27129258

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-229990 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Antibody Fab fragment heavy chain Chains: A, E
Molecule details ›
Chains: A, E
Length: 219 amino acids
Theoretical weight: 23.75 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Antibody Fab fragment light chain Chains: B, F
Molecule details ›
Chains: B, F
Length: 218 amino acids
Theoretical weight: 24.12 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Beta-theraphotoxin-Cm1a Chains: C, D
Molecule details ›
Chains: C, D
Length: 33 amino acids
Theoretical weight: 3.99 KDa
Source organism: Ceratogyrus marshalli
Expression system: Not provided
UniProt:
  • Canonical: P84507 (Residues: 1-33; Coverage: 100%)
Sequence domains: Ion channel inhibitory toxin

Ligands and Environments

No bound ligands
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.1
Spacegroup: P212121
Unit cell:
a: 97.322Å b: 98.438Å c: 107.35Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.219
Expression systems:
  • Homo sapiens
  • Not provided

Quick links

Citations

6 review citations

Status of peripheral sodium channel blockers for non-addictive pain treatment.
Alsaloum et al. (2020)
5 more

3 mentions without citation

Structure-Function and Therapeutic Potential of Spider Venom-Derived Cysteine Knot Peptides Targeting Sodium Channels.
Cardoso et al. (2019)
2 more