SAXSdb — 9d97

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

MHC class I antigen

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Beta-2-microglobulin × 1 （P61769） Cyclin-A2 × 1 （P20248） Killer cell immunoglobulin-like receptor 3DL1 × 1 （P43629） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Beta-2-microglobulin × 1 （P61769） Cyclin-A2 × 1 （P20248） Killer cell immunoglobulin-like receptor 3DL1 × 1 （P43629） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E5FQ58_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 25–300

Beta-2-microglobulin

Homo sapiens

UniProt P61769

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	MHC class I antigen × 1 （E5FQ58） Cyclin-A2 × 1 （P20248） Killer cell immunoglobulin-like receptor 3DL1 × 1 （P43629） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	MHC class I antigen × 1 （E5FQ58） Cyclin-A2 × 1 （P20248） Killer cell immunoglobulin-like receptor 3DL1 × 1 （P43629） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 4	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–100； UniProt 21–119

Cyclin-A2

Homo sapiens

UniProt P20248

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	MHC class I antigen × 1 （E5FQ58） Beta-2-microglobulin × 1 （P61769） Killer cell immunoglobulin-like receptor 3DL1 × 1 （P43629） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	MHC class I antigen × 1 （E5FQ58） Beta-2-microglobulin × 1 （P61769） Killer cell immunoglobulin-like receptor 3DL1 × 1 （P43629） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCNA2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–9； UniProt 178–186

Killer cell immunoglobulin-like receptor 3DL1

Homo sapiens

UniProt P43629

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	MHC class I antigen × 1 （E5FQ58） Beta-2-microglobulin × 1 （P61769） Cyclin-A2 × 1 （P20248） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	MHC class I antigen × 1 （E5FQ58） Beta-2-microglobulin × 1 （P61769） Cyclin-A2 × 1 （P20248） 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KI3L1_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain G； PDBConstruct 4–301； UniProt 23–320

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	9d97
Deposition date deposition_date	2024-08-21
Structure title title	KIR3DL1 - HLA-B*38-YHE complex
Keywords keywords	Killer Immunoglobulin-like receptor, Human Leucocyte Antigen, immune complex, NK cell, 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.

9d97__assembly_1__model_1

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

Download this curve (.dat)

9d97__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9d97__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.00 Å
Rg (electron density)	34.02 Å
Total Rg	34.38 Å
Atom count	5375
Residues	674
Excluded volume	94207 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9d97__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9d97__assembly_2__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	MHC class I antigen
Molecular weight formula_weight	32029.3 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	5961

GSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQICKTNTQTYRENLRIALRYYNQSEAGSHTLQRMYGCDVGPDGRLLRGHNQFAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRTYLEGTCVEWLRRYLENGKETLQRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Source Source

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

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11879.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Source Source

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

Entity 3 Entity 3 polymer

Description description	Cyclin-A2
Molecular weight formula_weight	1192.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

YHEDIHTYL

Source Source

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

Entity 4 Entity 4 polymer

Description description	Killer cell immunoglobulin-like receptor 3DL1
Molecular weight formula_weight	33220.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

GSHMGGQDKPFLSAWPSAVVPRGGHVTLRCHYRHRFNNFMLYKEDRIHIPIFHGRIFQESFNMSPVTTAHAGNYTCRGSHPHSPTGWSAPSNPVVIMVTGNHRKPSLLAHPGPLVKSGERVILQCWSDIMFEHFFLHKEGISKDPSRLVGQIHDGVSKANFSIGPMMLALAGTYRCYGSVTHTPYQLSAPSDPLDIVVTGPYEKPSLSAQPGPKVQAGESVTLSCSSRSSYDMYHLSREGGAHERRLPAVRKVNRTFQADFPLGPATHGGTYRCFGSFRHSPYEWSDPSDPLLVSVTGNPS

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 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	571

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Unit-cell length a length_a	46.963 Å
Unit-cell length b length_b	60.047 Å
Unit-cell length c length_c	63.337 Å
Unit-cell angle α angle_alpha	94.96 °
Unit-cell angle β angle_beta	95.50 °
Unit-cell angle γ angle_gamma	106.23 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	44.740 Å
R factor r_factor	0.1651
R_work r_work	0.1643
R_free r_free	0.1948

KIR3DL1 - HLA-B*38-YHE complex

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

MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Cyclin-A2

State in the Current Structure

Other States of the Same Protein in the Database

Killer cell immunoglobulin-like receptor 3DL1

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

9d97__assembly_1__model_1

9d97__assembly_1__model_1 | I(q)

9d97__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

KIR3DL1 - HLA-B*38-YHE complex

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

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

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cyclin-A2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Killer cell immunoglobulin-like receptor 3DL1

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

9d97__assembly_1__model_1

9d97__assembly_1__model_1 | I(q)

9d97__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)