Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47170.09 
• Atom Count: 3294 
• Residue Count: 402 
• Unique protein chains: 3

5NI9

Crystal structure of HLA-DRB1*04:01 with the alpha-enolase peptide 326-340

• DOI: 10.2210/pdb5NI9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2017-03-23 Released: 2018-06-13 
• Deposition Author(s): Gerstner, C., Dubnovitsky, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.176 
• R-Value Work: 0.146 

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

• PubMed: 29853344 
• Primary Citation of Related Structures:  
  5NIG

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DR alpha chain	A	189	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
HLA class II histocompatibility antigen, DRB1-4 beta chain	B	198	Homo sapiens	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
Alpha-enolase	C	15	Homo sapiens	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MRD	A	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
URE	A, B	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N
MPD	B, C	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.176 
• R-Value Work: 0.146 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 68.447	α = 90.00
b = 128.109	β = 90.00
c = 53.585	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
XDS	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-03-23 
• Released Date: 2018-06-13 
• Deposition Author(s): Gerstner, C., Dubnovitsky, A.

Revision History 

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