3PV6 | pdb_00003pv6

Crystal structure of NKp30 bound to its ligand B7-H6

• PDB DOI: https://doi.org/10.2210/pdb3PV6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-06 Released: 2011-03-16 
• Deposition Author(s): Li, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.289 (Depositor) 
• R-Value Work: 
  0.239 (Depositor), 0.239 (DCC) 

Literature

Structure of the activating natural killer cell receptor NKp30 bound to its ligand B7-H6 reveals basis for tumor cell recognition in humans

Li, Y., Wang, Q., Mariuzza, R.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.54 kDa 
• Atom Count: 2,611 
• Modeled Residue Count: 326 
• Deposited Residue Count: 365 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ig-like domain-containing protein DKFZp686O24166/DKFZp686I21167	A	248	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q68D85 (Homo sapiens) Explore Q68D85  Go to UniProtKB:  Q68D85
PHAROS:  Q68D85 GTEx:  ENSG00000188211
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q68D85-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Natural cytotoxicity triggering receptor 3	B	117	Homo sapiens	Mutation(s): 0  Gene Names: NCR3, 1C7, LY117
UniProt & NIH Common Fund Data Resources
Find proteins for O14931 (Homo sapiens) Explore O14931  Go to UniProtKB:  O14931
PHAROS:  O14931 GTEx:  ENSG00000204475

Oligosaccharides

Help

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.289 (Depositor) 
• R-Value Work:  0.239 (Depositor), 0.239 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.874	α = 90
b = 74.868	β = 90
c = 125.534	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Li, Y.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-11-27
  Changes: Data collection, Database references, Structure summary