5L9D: AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSYLATED, CRYSTAL FORM I, parsimonious model

Citation:
Abstract
The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the VL1 antigen-binding loop, with the alpha-1-6 core fucosylated complex glycan facing out of the L1 complementarity-determining region. The crystal structures of two non-apparent (pseudo) isomorphous crystals of the N14 Fab were analyzed, which differ significantly in the elbow angles, thereby cautioning against the overinterpretation of domain movements upon antigen binding. In addition, the map quality at 1.9 A resolution was sufficient to crystallographically re-sequence the variable VL and VH domains and to detect discrepancies in the hybridoma-derived sequence. Finally, a conservatively refined parsimonious model is presented and its statistics are compared with those from a less conservatively built model that has been modelled more enthusiastically. Improvements to the PDB validation reports affecting ligands, clashscore and buried surface calculations are suggested.
PDB ID: 5L9DDownload
MMDB ID: 141620
PDB Deposition Date: 2016/6/10
Updated in MMDB: 2017/12
Experimental Method:
x-ray diffraction
Resolution: 1.88  Å
Source Organism:
Similar Structures:
Biological Unit for 5L9D: dimeric; determined by software (PISA)
Molecular Components in 5L9D
Label Count Molecule
Proteins (2 molecules)
1
Mouse Antibody FAB Fragment, Igg1-kappa Heavy Chain
Molecule annotation
1
Mouse Antibody FAB Fragment, Igg1-kappa Light Chain
Molecule annotation
Chemicals (9 molecules)
1
2
2
1
3
1
4
3
5
1
6
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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