SAXSdb — 1qo3

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

MHC CLASS I H-2DD HEAVY CHAIN

MUS MUSCULUS

UniProt P01900

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	BETA-2-MICROGLOBULIN × 1 （P01887） LY49A × 2 （P20937） HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE × 1 （P04582） 1,2-ETHANEDIOL × 3 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	BETA-2-MICROGLOBULIN × 1 （P01887） LY49A × 2 （P20937） HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE × 1 （P04582） 1,2-ETHANEDIOL × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HA12_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–277； UniProt 26–301

BETA-2-MICROGLOBULIN

MUS MUSCULUS

UniProt P01887

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	MHC CLASS I H-2DD HEAVY CHAIN × 1 （P01900） LY49A × 2 （P20937） HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE × 1 （P04582） 1,2-ETHANEDIOL × 3 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	MHC CLASS I H-2DD HEAVY CHAIN × 1 （P01900） LY49A × 2 （P20937） HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE × 1 （P04582） 1,2-ETHANEDIOL × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B2MG_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–100； UniProt 21–119

LY49A

MUS MUSCULUS

UniProt P20937

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	MHC CLASS I H-2DD HEAVY CHAIN × 1 （P01900） BETA-2-MICROGLOBULIN × 1 （P01887） HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE × 1 （P04582） 1,2-ETHANEDIOL × 3 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	MHC CLASS I H-2DD HEAVY CHAIN × 1 （P01900） BETA-2-MICROGLOBULIN × 1 （P01887） HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE × 1 （P04582） 1,2-ETHANEDIOL × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LY4A_MOUSE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–137； UniProt 126–262 Author chain D； PDBConstruct 1–137； UniProt 126–262

HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE

OrganismNot specified

UniProt P04582

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	MHC CLASS I H-2DD HEAVY CHAIN × 1 （P01900） BETA-2-MICROGLOBULIN × 1 （P01887） LY49A × 2 （P20937） 1,2-ETHANEDIOL × 3 water × 5	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	MHC CLASS I H-2DD HEAVY CHAIN × 1 （P01900） BETA-2-MICROGLOBULIN × 1 （P01887） LY49A × 2 （P20937） 1,2-ETHANEDIOL × 3 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENV_HV1B8
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 1–10； UniProt 311–320

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	1qo3
Deposition date deposition_date	1999-11-01
Structure title title	Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd
Keywords keywords	;RECEPTOR/IMMUNE SYSTEM, COMPLEX (NK RECEPTOR-MHC CLASS I), NK CELL, INHIBITORY RECEPTOR, MHC-I, C-TYPE LECTIN-LIKE, HISTOCOMPATIBILITY, B2M, LY49, LY-49, RECEPTOR-IMMUNE SYSTEM complex ;; RECEPTOR/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.

1qo3__assembly_1__model_1

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

Download this curve (.dat)

1qo3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1qo3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.66 Å
Rg (electron density)	26.60 Å
Total Rg	27.44 Å
Atom count	5190
Residues	633
Excluded volume	91763 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1qo3__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1qo3__assembly_2__model_1`	pentameric （5）	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 H-2DD HEAVY CHAIN
Molecular weight formula_weight	32265.9 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	5542

MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLRTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGKE

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	BETA-2-MICROGLOBULIN
Molecular weight formula_weight	11791.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	LY49A
Molecular weight formula_weight	15921.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

STVLDSLQHTGRGDKVYWFCYGMKCYYFVMDRKTWSGCKQTCQSSSLSLLKIDDEDELKFLQLVVPSDSCWVGLSYDNKKKDWAWIDNRPSKLALNTRKYNIRDGGCMLLSKTRLDNGNCDQVFICICGKRLDKFPH

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 4 Entity 4 polymer

Description description	HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE
Molecular weight formula_weight	1075.3 kDa
Mutation mutation	YES
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

RGPGRAFVTI

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	352

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1qo3a1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1qo3a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d1qo3b2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1qo3b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1qo3c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1qo3d_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (5 domains)

Domain ID domain_id	1qo3A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	1qo3A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1qo3B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1qo3C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1qo3D00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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Unit-cell length a length_a	78.963 Å
Unit-cell length b length_b	96.957 Å
Unit-cell length c length_c	99.318 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2380

Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd

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

MHC CLASS I H-2DD HEAVY CHAIN

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

LY49A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HIV ENVELOPE GLYCOPROTEIN 120 PEPTIDE

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

1qo3__assembly_1__model_1

1qo3__assembly_1__model_1 | I(q)

1qo3__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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (6 domains)

CATH v4.4 (5 domains)

7. Citations (3)