6DDR

Crystal Structure Analysis of the Epitope of an Anti-MICA Antibody

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

High-resolution glycosylation site-engineering method identifies MICA epitope critical for shedding inhibition activity of anti-MICA antibodies.

Lombana, T.N., Matsumoto, M.L., Berkley, A.M., Toy, E., Cook, R., Gan, Y., Du, C., Schnier, P., Sandoval, W., Ye, Z., Schartner, J.M., Kim, J., Spiess, C.

(2019) MAbs 11: 75-93


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anti-MICA Fab fragment light chain clone 13A9
A
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anti-MICA Fab fragment heavy chain clone 13A9
B
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
MHC class I polypeptide-related sequence A
C
94Homo sapiensMutation(s): 0 
Gene Names: MICA
Find proteins for Q96QC4 (Homo sapiens)
Go to Gene View: MICA
Go to UniProtKB:  Q96QC4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4
Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.549α = 90.00
b = 61.833β = 90.00
c = 172.368γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2018-05-10 
  • Released Date: 2018-10-24 
  • Deposition Author(s): Matsumoto, M.L.

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-12-05
    Type: Data collection, Database references
  • Version 1.2: 2019-01-23
    Type: Data collection, Database references