6H6H

Crystal structures of the murine class I major histocompatibility complex H-2Dbm13 in complex with adenovirus-derived peptide Ad10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

wwPDB Validation 3D Report Full Report



Literature

Crystal structures of H-2Db and H-2Dbm13 with cancer-associated Ad 10 peptide reveal that subtle changes in the peptide environment impact thermostability and alloreactivity

Abualrous, E.T.Han, X.Badia-Martines, D.Sun, R.van Hall, T.Sandalova, T.Ossendorp, F.Achour, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2D cell surface glycoprotein
A, D
338Mus musculusMutation(s): 0 
Gene Names: H2-D1H-2DH2-L
Find proteins for Q31167 (Mus musculus)
Go to UniProtKB:  Q31167
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, E
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
NIH Common Fund Data Resources
IMPC  MGI:88127
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILE
C, F
10unidentified adenovirusMutation(s): 0 
Find proteins for P03255 (Human adenovirus C serotype 5)
Go to UniProtKB:  P03255
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.41α = 83.98
b = 70.27β = 86.9
c = 87.05γ = 81.75
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-14
    Type: Initial release