6ATF

HLA-DRB1*1402 in complex with Vimentin59-71


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis for increased susceptibility of Indigenous North Americans to seropositive rheumatoid arthritis.

Scally, S.W.Law, S.C.Ting, Y.T.Heemst, J.V.Sokolove, J.Deutsch, A.J.Bridie Clemens, E.Moustakas, A.K.Papadopoulos, G.K.Woude, D.V.Smolik, I.Hitchon, C.A.Robinson, D.B.Ferucci, E.D.Bernstein, C.N.Meng, X.Anaparti, V.Huizinga, T.Kedzierska, K.Reid, H.H.Raychaudhuri, S.Toes, R.E.Rossjohn, J.El-Gabalawy, H.Thomas, R.

(2017) Ann. Rheum. Dis. 76: 1915-1923


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A, D
189Homo sapiensGene Names: HLA-DRA (HLA-DRA1)
Find proteins for P01903 (Homo sapiens)
Go to Gene View: HLA-DRA
Go to UniProtKB:  P01903
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MHC class II antigen
B, E
200N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Vimentin59-71
C, F
13Homo sapiensGene Names: VIM
Find proteins for P08670 (Homo sapiens)
Go to Gene View: VIM
Go to UniProtKB:  P08670
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
B, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 66.980α = 90.00
b = 77.770β = 109.52
c = 94.540γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
NHMRC, ARCAustralia--

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references