5NIG

Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340 (arginine 327 to citrulline)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Memory T cells specific to citrullinated alpha-enolase are enriched in the rheumatic joint.

Pieper, J.Dubnovitsky, A.Gerstner, C.James, E.A.Rieck, M.Kozhukh, G.Tandre, K.Pellegrino, S.Gebe, J.A.Ronnblom, L.Sandalova, T.Kwok, W.W.Klareskog, L.Buckner, J.H.Achour, A.Malmstrom, V.

(2018) J. Autoimmun. 92: 47-56


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HLA class II histocompatibility antigen, DR alpha chain
A
189Homo sapiensMutation(s): 0 
Gene 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
HLA class II histocompatibility antigen, DRB1-4 beta chain
B
198Homo sapiensMutation(s): 0 
Gene Names: HLA-DRB1
Find proteins for P13760 (Homo sapiens)
Go to Gene View: HLA-DRB1
Go to UniProtKB:  P13760
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Alpha-enolase
C
15Homo sapiensMutation(s): 0 
Gene Names: ENO1 (ENO1L1, MBPB1, MPB1)
EC: 4.2.1.11
Find proteins for P06733 (Homo sapiens)
Go to Gene View: ENO1
Go to UniProtKB:  P06733
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
URE
Query on URE

Download SDF File 
Download CCD File 
B
UREA
C H4 N2 O
XSQUKJJJFZCRTK-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
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, C
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CIR
Query on CIR
C
L-PEPTIDE LINKINGC6 H13 N3 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.142 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 68.606α = 90.00
b = 128.319β = 90.00
c = 53.521γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-13
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references