› 3wih

X-ray diffraction
1.7Å resolution

Crystal structure of the third fibronectin domain (Fn3) of human ROBO1 in complex with the Fab fragment of murine monoclonal antibody B2212A.

Released:
DOI: 10.2210/pdb3wih/pdb
PDB entry 3wih coloured by chain, front view.
PDB entry 3wih coloured by chain, side view.
PDB entry 3wih coloured by chain, top view.
Source organisms:
Primary publication:
Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses.
Nakayama T, Mizohata E, Yamashita T, Nagatoishi S, Nakakido M, Iwanari H, Mochizuki Y, Kado Y, Yokota Y, Satoh R, Tsumoto K, Fujitani H, Kodama T, Hamakubo T, Inoue T
Protein Sci 24 328-40 (2015)
PMID: 25492858

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-235417 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Roundabout homolog 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 97 amino acids
Theoretical weight: 10.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y6N7 (Residues: 777-873; Coverage: 6%)
Gene names: DUTT1, ROBO1
Sequence domains: Fibronectin type III domain
Structure domains: Immunoglobulins
anti-human ROBO1 antibody B2212A Fab light chain Chains: L, M
Molecule details ›
Chains: L, M
Length: 213 amino acids
Theoretical weight: 23.57 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
anti-human ROBO1 antibody B2212A Fab heavy chain Chains: H, I
Molecule details ›
Chains: H, I
Length: 219 amino acids
Theoretical weight: 23.73 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: C2
Unit cell:
a: 159.474Å b: 102.601Å c: 97.236Å
α: 90° β: 127.57° γ: 90°
R-values:
R R work R free
0.192 0.189 0.236
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Toward rational antibody design: recent advancements in molecular dynamics simulations.
Yamashita T. (2018)
1 more

1 mention without citation

Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses.
Nakayama et al. (2015)