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


This is version 1.1 of the entry. See complete history


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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
H-2D cell surface glycoproteinA,
B [auth D]
338Mus musculusMutation(s): 0 
Gene Names: H2-D1H-2DH2-L
UniProt
Find proteins for Q31167 (Mus musculus)
Explore Q31167 
Go to UniProtKB:  Q31167
Entity Groups  
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UniProt GroupQ31167
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulinC [auth B],
D [auth E]
99Mus musculusMutation(s): 0 
Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus)
Explore P01887 
Go to UniProtKB:  P01887
IMPC:  MGI:88127
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UniProt GroupP01887
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SER-GLY-PRO-SER-ASN-THR-PRO-PRO-GLU-ILEE [auth C],
F
10unidentified adenovirusMutation(s): 0 
UniProt
Find proteins for P03255 (Human adenovirus C serotype 5)
Explore P03255 
Go to UniProtKB:  P03255
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UniProt GroupP03255
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
N [auth D],
O [auth D],
P [auth D],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth E],
W [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description