4NO3

Crystal structure of AMPD2 phosphopeptide bound to HLA-A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.703 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status.

Stones, D.H.Zarling, A.L.Willcox, C.R.Shabanowitz, J.Cummings, K.L.Hunt, D.F.Cobbold, M.Engelhard, V.H.Willcox, B.E.Mohammed, F.

(2017) Oncotarget --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class I histocompatibility antigen, A-2 alpha chain
A
274Homo sapiensMutation(s): 0 
Gene Names: HLA-A (HLAA)
Find proteins for P01892 (Homo sapiens)
Go to Gene View: HLA-A
Go to UniProtKB:  P01892
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-2-microglobulin
B
99Homo sapiensMutation(s): 0 
Gene Names: B2M
Find proteins for P61769 (Homo sapiens)
Go to Gene View: B2M
Go to UniProtKB:  P61769
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
AMP deaminase 2
C
9Homo sapiensMutation(s): 0 
Gene Names: AMPD2
EC: 3.5.4.6
Find proteins for Q01433 (Homo sapiens)
Go to Gene View: AMPD2
Go to UniProtKB:  Q01433
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
C
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.703 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.000α = 90.00
b = 55.200β = 104.90
c = 75.100γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
d*TREKdata scaling
MOLREPphasing
XSCALEdata scaling
REFMACrefinement
CrystalCleardata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2017-05-24
    Type: Database references