› 6a79

X-ray diffraction
2.31Å resolution

Crystal structure of the fifth immunoglobulin domain (Ig5) of human Robo1 in complex with the mutant scFv fragment (P103A) of murine monoclonal antibody B5209B

Released:
DOI: 10.2210/pdb6a79/pdb
PDB entry 6a79 coloured by chain, front view.
PDB entry 6a79 coloured by chain, side view.
PDB entry 6a79 coloured by chain, top view.
Source organisms:
Primary publication:
Affinity Improvement of a Cancer-Targeted Antibody through Alanine-Induced Adjustment of Antigen-Antibody Interface.
Yamashita T, Mizohata E, Nagatoishi S, Watanabe T, Nakakido M, Iwanari H, Mochizuki Y, Nakayama T, Kado Y, Yokota Y, Matsumura H, Kawamura T, Kodama T, Hamakubo T, Inoue T, Fujitani H, Tsumoto K
Structure 27 519-527.e5 (2019)
PMID: 30595454

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Roundabout homolog 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 91 amino acids
Theoretical weight: 9.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y6N7 (Residues: 455-543; Coverage: 6%)
Gene names: DUTT1, ROBO1
Sequence domains: Immunoglobulin domain
Structure domains: Immunoglobulins
Light chain region of the anti-human Robo1 antibody B5209B scFv Chains: L, M
Molecule details ›
Chains: L, M
Length: 112 amino acids
Theoretical weight: 12 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
Heavy chain of the anti-human Robo1 antibody B5209B scFv Chains: H, I
Molecule details ›
Chains: H, I
Length: 138 amino acids
Theoretical weight: 14.35 KDa
Source organism: Mus musculus
Expression system: Escherichia coli

Ligands and Environments

1 bound ligand:
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21212
Unit cell:
a: 70.766Å b: 150.219Å c: 66.852Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.274 0.273 0.295
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Phage Display Technology as a Powerful Platform for Antibody Drug Discovery.
Nagano et al. (2021)
2 more