8QMD | pdb_00008qmd

Human NK cell receptor NKp80, extracellular domain

PDB DOI: https://doi.org/10.2210/pdb8QMD/pdb

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

Deposited: 2023-09-22 Released: 2025-04-02
Deposition Author(s): Blaha, J., Pazderova, K., Kalouskova, B., Wilmanns, M., Vanek, O.
Funding Organization(s): Czech Science Foundation, European Union (EU), Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.221 (Depositor), 0.221 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of the human NK cell activation receptor NKp80 ectodomain

Pazderova, K., Kalouskova, B., Blaha, J., Wilmanns, M., Vanek, O.

To be published.

Macromolecule Content

Total Structure Weight: 212.52 kDa
Atom Count: 10,402
Modeled Residue Count: 1,230
Deposited Residue Count: 1,820
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Killer cell lectin-like receptor subfamily F member 1	A [auth C] B [auth D] C [auth A] D [auth B] E A [auth C], B [auth D], C [auth A], D [auth B], E, F, G, H, I, J	182	Homo sapiens	Mutation(s): 1 Gene Names: KLRF1, CLEC5C, ML
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZS2 (Homo sapiens) Explore Q9NZS2 Go to UniProtKB: Q9NZS2
PHAROS: Q9NZS2 GTEx: ENSG00000150045
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NZS2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth C] Focus chain B [auth D] Focus chain C [auth A] Focus chain D [auth B] Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J	Go to GlyGen: Q9NZS2-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain T [auth J] SDF format, chain S [auth I] SDF format, chain R [auth H] SDF format, chain Q [auth G] SDF format, chain P [auth F] SDF format, chain O [auth E] SDF format, chain N [auth B] SDF format, chain M [auth A] SDF format, chain L [auth D] SDF format, chain K [auth C] MOL2 format, chain T [auth J] MOL2 format, chain S [auth I] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain P [auth F] MOL2 format, chain O [auth E] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] mmCIF format, chain T [auth J] mmCIF format, chain S [auth I] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain P [auth F] mmCIF format, chain O [auth E] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C]	K [auth C] L [auth D] M [auth A] N [auth B] O [auth E] K [auth C], L [auth D], M [auth A], N [auth B], O [auth E], P [auth F], Q [auth G], R [auth H], S [auth I], T [auth J]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J] Interactions & Density Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Focus chain S [auth I] Focus chain T [auth J]