SAXSdb — 5hga

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

HLA class I histocompatibility antigen, A-24 alpha chain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P61769） 8-mer from Protein Nef × 1 （P18801） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Beta-2-microglobulin × 1 （P61769） 8-mer from Protein Nef × 1 （P18801） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	1A24_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–275； UniProt 25–298 Author chain D； PDBConstruct 2–275； UniProt 25–298

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 3	HLA class I histocompatibility antigen, A-24 alpha chain × 1 （P05534） 8-mer from Protein Nef × 1 （P18801） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	HLA class I histocompatibility antigen, A-24 alpha chain × 1 （P05534） 8-mer from Protein Nef × 1 （P18801） water × 3	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 Author chain E； PDBConstruct 2–100； UniProt 21–119

8-mer from Protein Nef

OrganismNot specified

UniProt P18801

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	HLA class I histocompatibility antigen, A-24 alpha chain × 1 （P05534） Beta-2-microglobulin × 1 （P61769） water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	HLA class I histocompatibility antigen, A-24 alpha chain × 1 （P05534） Beta-2-microglobulin × 1 （P61769） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NEF_HV1ND
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–8； UniProt 135–142 Author chain F； PDBConstruct 1–8； UniProt 135–142

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	5hga
Deposition date deposition_date	2016-01-08
Structure title title	HLA*A2402 complex with HIV nef138 Y2F-8mer mutant epitope
Keywords keywords	HLA, Antigen presentation, HIV, 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.

5hga__assembly_1__model_1

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

Download this curve (.dat)

5hga__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5hga__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.95 Å
Rg (electron density)	22.81 Å
Total Rg	23.66 Å
Atom count	3131
Residues	382
Excluded volume	54702 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5hga__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5hga__assembly_2__model_1`	trimeric （3）	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	HLA class I histocompatibility antigen, A-24 alpha chain
Molecular weight formula_weight	31683.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	6416

MGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

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 'BL21-Gold(DE3)pLysS AG' ;

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	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 Entity 3 polymer

Description description	8-mer from Protein Nef
Molecular weight formula_weight	1024.2 kDa
Mutation mutation	Y2F
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

RFPLTFGW

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	154

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5hgaA01
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	5hgaA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5hgaB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5hgaD01
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	5hgaD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5hgaE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	64.838 Å
Unit-cell length b length_b	86.913 Å
Unit-cell length c length_c	151.441 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	2.199 Å
Low-resolution limit resolution_low	37.860 Å
R factor r_factor	0.2075
R_work r_work	0.2053
R_free r_free	0.2498

HLA*A2402 complex with HIV nef138 Y2F-8mer mutant epitope

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

HLA class I histocompatibility antigen, A-24 alpha chain

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

8-mer from Protein Nef

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

5hga__assembly_1__model_1

5hga__assembly_1__model_1 | I(q)

5hga__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

HLA*A2402 complex with HIV nef138 Y2F-8mer mutant epitope

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

HLA class I histocompatibility antigen, A-24 alpha 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

8-mer from Protein Nef

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

5hga__assembly_1__model_1

5hga__assembly_1__model_1 | I(q)

5hga__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)