3NOI

Crystal Structure of Natural Killer Cell Cytotoxicity Receptor NKp30 (NCR3)

PDB DOI: https://doi.org/10.2210/pdb3NOI/pdb

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

Deposited: 2010-06-25 Released: 2011-03-30
Deposition Author(s): Joyce, M.G., Sun, P.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.204 (Depositor), 0.220 (DCC)
R-Value Work:
0.164 (Depositor), 0.190 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure of the Natural Killer cell activating receptor NKp30 and dissection of ligand binding site

Joyce, M.G., Tran, P., Zhuravleva, M.A., Jaw, J., Colonna, M., Sun, P.D.

(2011) Proc Natl Acad Sci U S A

Macromolecule Content

Total Structure Weight: 27.54 kDa
Atom Count: 2,140
Modelled Residue Count: 239
Deposited Residue Count: 240
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Natural cytotoxicity triggering receptor 3	A, B	120	Homo sapiens	Mutation(s): 0 Gene Names: NKp30, 1C7, LY117, NCR3
UniProt & NIH Common Fund Data Resources
Find proteins for O14931 (Homo sapiens) Explore O14931 Go to UniProtKB: O14931
PHAROS: O14931 GTEx: ENSG00000204475
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14931
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PG Query on 1PG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	H [auth A], K [auth B], L [auth B]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C₁₁ H₂₄ O₆ SLNYBUIEAMRFSZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.204 (Depositor), 0.220 (DCC)
R-Value Work: 0.164 (Depositor), 0.190 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.1	α = 90
b = 53.02	β = 107.73
c = 51.952	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-03-30

Deposition Author(s):

Joyce, M.G.

Sun, P.D.

Revision History (Full details and data files)

Version 1.0: 2011-03-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.3: 2024-10-30
Changes: Structure summary