› 5gir

X-ray diffraction
1.93Å resolution

Crystal structure of a Fab fragment with its ligand peptide

Released:
DOI: 10.2210/pdb5gir/pdb
PDB entry 5gir coloured by chain, front view.
PDB entry 5gir coloured by chain, side view.
PDB entry 5gir 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-234998 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Heavy chain of Fab fragment Chains: A, H
Molecule details ›
Chains: A, 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 Chains: B, L
Molecule details ›
Chains: B, L
Length: 234 amino acids
Theoretical weight: 26.01 KDa
Source organism: Mus musculus
Expression system: Mammalia
Structure domains: Immunoglobulins
Isocitrate dehydrogenase [NADP] cytoplasmic Chains: C, D
Molecule details ›
Chains: C, D
Length: 12 amino acids
Theoretical weight: 1.27 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: O75874 (Residues: 126-137; Coverage: 3%)
Gene names: IDH1, PICD

Ligands and Environments

2 bound ligands:
Ligand SO4 9 x SO4
Ligand EDO 2 x EDO
1 modified residue:
Ligand PCA 2 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44XU
Spacegroup: P21
Unit cell:
a: 69.11Å b: 93.65Å c: 70.56Å
α: 90° β: 107.51° γ: 90°
R-values:
R R work R free
0.184 0.182 0.231
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)