3ROL

Murine class I major histocompatibility complex H-2Kb in complex with post-translationally modified LCMV-derived gp34-41 peptide, comprising a nitrotyrosine at position 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Nitro-tyrosination of the immunodominant LCMV epitope gp34-41 alters both its capacity to stabilize H-2Kb and the molecular surface of the MHC complex, affecting TCR recognition

Madhurantakam, C.Duru, A.D.Leong, C.Sandalova, T.Webb, J.R.Achour, A.

(2012) PLoS ONE --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class I histocompatibility antigen, K-B alpha chain
A, C
275Mus musculusMutation(s): 0 
Gene Names: H2-K1 (H2-K)
Find proteins for P01901 (Mus musculus)
Go to UniProtKB:  P01901
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B, D
99Mus musculusMutation(s): 0 
Gene Names: B2m
Find proteins for P01887 (Mus musculus)
Go to UniProtKB:  P01887
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pre-glycoprotein polyprotein GP complex
E, F
8Lymphocytic choriomeningitis virus (strain WE)Mutation(s): 1 
Gene Names: GPC (GP-C)
Find proteins for P07399 (Lymphocytic choriomeningitis virus (strain WE))
Go to UniProtKB:  P07399
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
A, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
D
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NIY
Query on NIY
E, F
L-PEPTIDE LINKINGC9 H10 N2 O5TYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 50.466α = 90.00
b = 88.496β = 94.71
c = 119.050γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release