4QKI

Dimeric form of human LLT1, a ligand for NKR-P1

• PDB DOI: https://doi.org/10.2210/pdb4QKI/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2014-06-06 Released: 2015-03-11 
• Deposition Author(s): Skalova, T., Blaha, J., Harlos, K., Duskova, J., Koval, T., Stransky, J., Hasek, J., Vanek, O., Dohnalek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.27 kDa 
• Atom Count: 2,228 
• Modelled Residue Count: 242 
• Deposited Residue Count: 270 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 2 member D	A, B	135	Homo sapiens	Mutation(s): 1  Gene Names: CLAX, CLEC2B, CLEC2D, LLT1, OCIL
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHP7 (Homo sapiens) Explore Q9UHP7  Go to UniProtKB:  Q9UHP7
PHAROS:  Q9UHP7 GTEx:  ENSG00000069493

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth B], F [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: 1.80 Å
• R-Value Free: 0.244 
• R-Value Work: 0.178 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.15785/SBGRID/723

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.26	α = 90
b = 54.12	β = 90
c = 74.22	γ = 90

Software Package:

Software Name	Purpose
BALBES	phasing
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-11 
Deposition Author(s): Skalova, T., Blaha, J., Harlos, K., Duskova, J., Koval, T., Stransky, J., Hasek, J., Vanek, O., Dohnalek, J.

Revision History  

• Version 1.0: 2015-03-11
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 1.2: 2018-06-13
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2018-06-20
  Changes: Data collection, Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary