5VU0

Crystal structure of the complex between afucosylated/galactosylated human IgG1 Fc and Fc gamma receptor IIIa (CD16A) with Man5 N-glycans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Antibody Fucosylation Lowers the Fc gamma RIIIa/CD16a Affinity by Limiting the Conformations Sampled by the N162-Glycan.

Falconer, D.J.Subedi, G.P.Marcella, A.M.Barb, A.W.

(2018) ACS Chem. Biol. 13: 2179-2189


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin gamma-1 heavy chain
A, B
217Homo sapiensMutation(s): 0 
Find proteins for P0DOX5 (Homo sapiens)
Go to UniProtKB:  P0DOX5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Low affinity immunoglobulin gamma Fc region receptor III-A
C
172Homo sapiensMutation(s): 4 
Gene Names: FCGR3A (CD16A, FCG3, FCGR3, IGFR3)
Find proteins for P08637 (Homo sapiens)
Go to Gene View: FCGR3A
Go to UniProtKB:  P08637
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
GAL
Query on GAL

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Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 124.069α = 90.00
b = 48.846β = 103.77
c = 134.927γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-3000data scaling
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--
Argonne National LaboratoryUnited StatesGUP-48455

Revision History 

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references
  • Version 1.2: 2018-08-08
    Type: Data collection, Database references
  • Version 1.3: 2018-08-29
    Type: Data collection, Database references