› 5xcv

X-ray diffraction
2.14Å resolution

Crystal structure of NZ-1 Fv-clasp fragment with its antigen peptide

Released:
DOI: 10.2210/pdb5xcv/pdb
PDB entry 5xcv coloured by chain, front view.
PDB entry 5xcv coloured by chain, side view.
PDB entry 5xcv coloured by chain, top view.
Source organisms:
Primary publication:
Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability.
Arimori T, Kitago Y, Umitsu M, Fujii Y, Asaki R, Tamura-Kawakami K, Takagi J
Structure 25 1611-1622.e4 (2017)
PMID: 28919443

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212550 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
VH(S112C)-SARAH chimera,VH(S112C)-SARAH chimera Chains: A, D
Molecule details ›
Chains: A, D
Length: 172 amino acids
Theoretical weight: 19.37 KDa
Source organism: Rattus
Expression system: Escherichia coli
VL-SARAH(S37C) chimera,VL-SARAH(S37C) chimera Chains: B, E
Molecule details ›
Chains: B, E
Length: 165 amino acids
Theoretical weight: 18.59 KDa
Source organism: Rattus
Expression system: Escherichia coli
Podoplanin Chains: C, F
Molecule details ›
Chains: C, F
Length: 14 amino acids
Theoretical weight: 1.35 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q86YL7 (Residues: 38-51; Coverage: 10%)
Gene names: GP36, PDPN, PSEC0003, PSEC0025

Ligands and Environments

1 bound ligand:
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: C2
Unit cell:
a: 145.617Å b: 50.122Å c: 121.868Å
α: 90° β: 110.46° γ: 90°
R-values:
R R work R free
0.231 0.228 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Solubility, Stability, and Avidity of Recombinant Antibody Fragments Expressed in Microorganisms.
Kang et al. (2020)
1 more