4NNX

Crystal structure of PKD2 phosphopeptide bound to HLA-A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.104 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 

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.

Mohammed, F.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.

(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
Serine/threonine-protein kinase D2
C
9Homo sapiensMutation(s): 0 
Gene Names: PRKD2 (PKD2)
EC: 2.7.11.13
Find proteins for Q9BZL6 (Homo sapiens)
Go to Gene View: PRKD2
Go to UniProtKB:  Q9BZL6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

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

Download SDF File 
Download CCD File 
A, B
CADMIUM ION
Cd
WLZRMCYVCSSEQC-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: 2.104 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.100α = 90.00
b = 79.800β = 90.00
c = 111.300γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
CrystalCleardata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2017-05-24
    Type: Database references