› 6a77

X-ray diffraction
2Å resolution

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

Released:
DOI: 10.2210/pdb6a77/pdb
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PDB entry 6a77 coloured by chain, front view.
PDB entry 6a77 coloured by chain, side view.
PDB entry 6a77 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)
Assembly name:
PDBe Complex ID:
PDB-CPX-212894 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Roundabout homolog 1 Chain: A
Molecule details ›
Chain: A
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 of the anti-human Robo1 antibody B5209B Fab Chain: L
Molecule details ›
Chain: L
Length: 211 amino acids
Theoretical weight: 23.1 KDa
Source organism: Mus musculus
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Heavy chain of the anti-human Robo1 antibody B5209B Fab Chain: H

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P43212
Unit cell:
a: 100.566Å b: 100.566Å c: 122.756Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.24 0.238 0.278
Expression systems:
  • Escherichia coli
  • Homo sapiens

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Citations

4 review citations

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

1 mention without citation

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants.
Guest et al. (2021)

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