SAXSdb — 9c6x

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–124； UniProt 21–119

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

Homo sapiens

UniProt Q9NX02

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NALP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–9； UniProt 323–331

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

Homo sapiens

UniProt R5AK10

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R5AK10_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 145–418； UniProt 25–298

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9c6x
Deposition date deposition_date	2024-06-09
Structure title title	Crystal Structure of a single chain trimer composed of HLA-B*39:01 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2
Keywords keywords	HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-39 ALPHA CHAIN, BETA-2-MICROGLOBULIN, NLRP2, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9c6x__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9c6x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9c6x__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.07 Å
Rg (electron density)	22.93 Å
Total Rg	23.81 Å
Atom count	3181
Residues	390
Excluded volume	55475 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9c6x__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen
Molecular weight formula_weight	46766.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3472

NRVMLPKAAGCGASGGGGSGGGGSMIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQICKTNTQTDRESLRNLRGCYNQSEAGSHTLQRMYGCDVGPDGRLLRGHNQFAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRTYLEGTCVEWLRRYLENGKETLQRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
Molecular weight formula_weight	162.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

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Unit-cell length a length_a	75.939 Å
Unit-cell length b length_b	84.123 Å
Unit-cell length c length_c	150.421 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	24.830 Å
R factor r_factor	0.2036
R_work r_work	0.2021
R_free r_free	0.2321

Crystal Structure of a single chain trimer composed of HLA-B*39:01 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2

1. Protein Identity and Related Structures Protein Identity & Related Structures

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9c6x__assembly_1__model_1

9c6x__assembly_1__model_1 | I(q)

9c6x__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal Structure of a single chain trimer composed of HLA-B*39:01 Y84C variant, beta-2microglobulin, and NRVMLPKAA peptide from NLRP2

1. Protein Identity and Related Structures Protein Identity & Related Structures

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NACHT, LRR and PYD domains-containing protein 2,Beta-2-microglobulin,MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9c6x__assembly_1__model_1

9c6x__assembly_1__model_1 | I(q)

9c6x__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)