9H8R | pdb_00009h8r

Crystal structure of Nkp46 in complex with a bicyclic peptide BCY00016132

• PDB DOI: https://doi.org/10.2210/pdb9H8R/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-29 Released: 2025-10-08 
• Deposition Author(s): Pellegrino, S., Carr, K., Bezerra, G.A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.239 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Nkp46 in complex with a bicyclic peptide BCY00016132

Pellegrino, S., Bezerra, G.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 25.38 kDa 
• Atom Count: 1,845 
• Modeled Residue Count: 202 
• Deposited Residue Count: 217 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Natural cytotoxicity triggering receptor 1	A	201	Homo sapiens	Mutation(s): 0  Gene Names: NCR1, LY94
UniProt & NIH Common Fund Data Resources
Find proteins for O76036 (Homo sapiens) Explore O76036  Go to UniProtKB:  O76036
PHAROS:  O76036 GTEx:  ENSG00000189430

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bicyclic peptide BCY00016132	B	16	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LFI	E [auth B]	1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one C12 H18 Br3 N3 O3 UYNTZRFVDTZUQI-UHFFFAOYSA-N
DHL	D [auth A]	2-AMINO-ETHANETHIOL C2 H7 N S UFULAYFCSOUIOV-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.239 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.688	α = 90
b = 74.688	β = 90
c = 75.307	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Pellegrino, S., Carr, K., Bezerra, G.A.

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release