6DIG

Crystal structure of DQA1*01:02/DQB1*06:02 in complex with a hypocretin peptide

• PDB DOI: https://doi.org/10.2210/pdb6DIG/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2018-05-23 Released: 2019-05-08 
• Deposition Author(s): Birtley, J.R., Stern, L.J., Mellins, E.D., Jiang, W.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 49.81 kDa 
• Atom Count: 3,372 
• Modelled Residue Count: 375 
• Deposited Residue Count: 435 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II HLA-DQ-alpha chain	A	207	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQA1
UniProt
Find proteins for Q30066 (Homo sapiens) Explore Q30066  Go to UniProtKB:  Q30066

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DQ beta 1 chain	B	215	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DQB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SU54 (Homo sapiens) Explore Q5SU54  Go to UniProtKB:  Q5SU54
GTEx:  ENSG00000179344

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
13-mer peptide: ALA-GLY-ASN-HIS-ALA-ALA-GLY-ILE-LEU-THR-LEU-GLY-LYS	C	13	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.255 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.666	α = 90
b = 89.596	β = 99.517
c = 90.928	γ = 90

Software Package:

Software Name	Purpose
phenix.refine	refinement
PHENIX	refinement
xia2	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-08 
Deposition Author(s): Birtley, J.R., Stern, L.J., Mellins, E.D., Jiang, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	5 U01 AI101990

Revision History  

• Version 1.0: 2019-05-08
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Database references, Structure summary
• Version 1.2: 2019-12-04
  Changes: Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary