› 5gis

X-ray diffraction
1.93Å resolution

Crystal structure of a Fab fragment with its ligand peptide

Released:
DOI: 10.2210/pdb5gis/pdb
PDB entry 5gis coloured by chain, front view.
PDB entry 5gis coloured by chain, side view.
PDB entry 5gis coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for multi-specific peptide recognition by the anti-IDH1/2 monoclonal antibody, MsMab-1.
Kitago Y, Kaneko MK, Ogasawara S, Kato Y, Takagi J
Biochem Biophys Res Commun 478 1274-9 (2016)
PMID: 27553275

Function and Biology Details

Reaction catalysed: 
(1a) isocitrate + NADP(+) = 2-oxalosuccinate + NADPH
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-235095 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Heavy chain of Fab fragment Chain: H
Molecule details ›
Chain: H
Length: 240 amino acids
Theoretical weight: 25.71 KDa
Source organism: Mus musculus
Expression system: Mammalia
Structure domains: Immunoglobulins
Light chain of Fab fragment Chain: L
Molecule details ›
Chain: L
Length: 234 amino acids
Theoretical weight: 26.01 KDa
Source organism: Mus musculus
Expression system: Mammalia
Structure domains: Immunoglobulins
Isocitrate dehydrogenase [NADP], mitochondrial Chain: C
Molecule details ›
Chain: C
Length: 16 amino acids
Theoretical weight: 1.76 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P48735 (Residues: 165-180; Coverage: 4%)
Gene name: IDH2

Ligands and Environments

1 bound ligand:
Ligand SO4 3 x SO4
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 57.05Å b: 65Å c: 67.13Å
α: 90° β: 111.8° γ: 90°
R-values:
R R work R free
0.188 0.186 0.216
Expression systems:
  • Mammalia
  • Not provided

Quick links

Citations

1 citations in other articles

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.
Miyanabe et al. (2018)

1 mention without citation

Second transmembrane helix (M2) and long range coupling in Ca²⁺-ATPase.
Daiho et al. (2014)