6NIX | pdb_00006nix

Crystal structure of Immune Receptor

• PDB DOI: https://doi.org/10.2210/pdb6NIX/pdb

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


• Deposited: 2019-01-01 Released: 2020-01-22 
• Deposition Author(s): Ting, Y.T., Reid, H.H., Rossjohn, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.235 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Immune Receptor

Ting, Y.T., Reid, H.H., Rossjohn, J.

To be published.

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: 47.56 kDa 
• Atom Count: 3,328 
• Modeled Residue Count: 380 
• Deposited Residue Count: 404 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A	189	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P01903-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DRB1-4 beta chain	B	200	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
PHAROS:  P01911 GTEx:  ENSG00000196126
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P01911-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Type II Collagen	C	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02458 (Homo sapiens) Explore P02458  Go to UniProtKB:  P02458
PHAROS:  P02458 GTEx:  ENSG00000139219

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	F [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
NAG	D [auth A], E [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.235 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.92	α = 90
b = 178.038	β = 90
c = 76.239	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Ting, Y.T., Reid, H.H., Rossjohn, J.

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-10-09
  Changes: Structure summary