› 5yd4

X-ray diffraction
1.35Å resolution

Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation T6A)

Released:
DOI: 10.2210/pdb5yd4/pdb
PDB entry 5yd4 coloured by chain, front view.
PDB entry 5yd4 coloured by chain, side view.
PDB entry 5yd4 coloured by chain, top view.
Source organisms:
Primary publication:
Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.
Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K
J Biochem 164 65-76 (2018)
PMID: 29924367

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-208459 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ig kappa chain V-II region 7S34.1 Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 251 amino acids
Theoretical weight: 26.75 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01630 (Residues: 1-112; Coverage: 99%)
Sequence domains: Immunoglobulin V-set domain
C-C chemokine receptor type 5 Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 9 amino acids
Theoretical weight: 1.07 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P51681 (Residues: 11-19; Coverage: 3%)
Gene names: CCR5, CMKBR5

Ligands and Environments

1 bound ligand:
Ligand SO4 8 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P21
Unit cell:
a: 80.47Å b: 72.9Å c: 86.46Å
α: 90° β: 114.15° γ: 90°
R-values:
R R work R free
0.136 0.135 0.173
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

4 citation in other articles

Immunotargeting of Nanocrystals by SpyCatcher Conjugation of Engineered Antibodies.
Pedroso et al. (2021)
3 more