5L9D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling.

Naschberger, A.Furnrohr, B.G.Lenac Rovis, T.Malic, S.Scheffzek, K.Dieplinger, H.Rupp, B.

(2016) Acta Crystallogr D Struct Biol 72: 1267-1280

  • DOI: 10.1107/S205979831601723X
  • Structures With Same Primary Citation

  • PubMed 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 r ...

    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 V L 1 antigen-binding loop, with the α-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 Å resolution was sufficient to crystallographically re-sequence the variable V L and V H 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.


    Organizational Affiliation

    Division of Genetic Epidemiology, Medical University of Innsbruck, Schöpfstrasse 41, 6020 Innsbruck, Austria.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MOUSE ANTIBODY FAB FRAGMENT, IGG1-KAPPA HEAVY CHAINH220Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MOUSE ANTIBODY FAB FRAGMENT, IGG1-KAPPA LIGHT CHAINL215Mus musculusMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE8
Query on PE8

Download CCD File 
H
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
L
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PG4
Query on PG4

Download CCD File 
H
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download CCD File 
H
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download CCD File 
H, L
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download CCD File 
H
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.782α = 90
b = 69.249β = 90
c = 87.803γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
BALBESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP28395-B26

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-11-16
    Changes: Data collection
  • Version 1.2: 2016-12-07
    Changes: Database references
  • Version 1.3: 2016-12-21
    Changes: Database references
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.5: 2017-11-22
    Changes: Database references
  • Version 1.6: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary