SAXSdb — 3c5j

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

HLA class II histocompatibility antigen, DR alpha chain

Homo sapiens

UniProt P01903

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MHC class II antigen × 1 （Q6YJU6） Elongation factor 1-alpha 2 × 1 （Q05639） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SULFATE ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	MHC class II antigen × 2 （Q6YJU6） Elongation factor 1-alpha 2 × 2 （Q05639） 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SULFATE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	2DRA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–181； UniProt 26–206

MHC class II antigen

Homo sapiens

UniProt Q6YJU6

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 II histocompatibility antigen, DR alpha chain × 1 （P01903） Elongation factor 1-alpha 2 × 1 （Q05639） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SULFATE ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	HLA class II histocompatibility antigen, DR alpha chain × 2 （P01903） Elongation factor 1-alpha 2 × 2 （Q05639） 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SULFATE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6YJU6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–190； UniProt 30–219

Elongation factor 1-alpha 2

Homo sapiens

UniProt Q05639

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 II histocompatibility antigen, DR alpha chain × 1 （P01903） MHC class II antigen × 1 （Q6YJU6） 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SULFATE ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	HLA class II histocompatibility antigen, DR alpha chain × 2 （P01903） MHC class II antigen × 2 （Q6YJU6） 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SULFATE ION × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EF1A2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–13； UniProt 343–355

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	3c5j
Deposition date deposition_date	2008-01-31
Structure title title	Crystal structure of HLA DR52c
Keywords keywords	;HLA, MHC class II, Glycoprotein, Immune response, Membrane, MHC II, Transmembrane, Elongation factor, GTP-binding, Methylation, Nucleotide-binding, Nucleus, Phosphoprotein, Protein biosynthesis, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
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.

3c5j__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3c5j__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c5j__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	32.73 Å
Rg (electron density)	32.26 Å
Total Rg	32.74 Å
Atom count	6198
Residues	746
Excluded volume	109450 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c5j__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3c5j__assembly_2__model_1`	hexameric （6）	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	HLA class II histocompatibility antigen, DR alpha chain
Molecular weight formula_weight	21084.8 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	3553

IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	MHC class II antigen
Molecular weight formula_weight	22121.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GDTRPRFLELLKSECHFFNGTERVRFLERYFHNQEEFVRFDSDVGEYRAVTELGRPVAESWNSQKDLLEQKRGQVDNYCRHNYGVVESFTVQRRVHPQVTVYPAKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIHNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Elongation factor 1-alpha 2
Molecular weight formula_weight	1390.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QVIILNHPGQISA

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	454

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3c5ja1
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	d3c5ja2
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	d3c5jb1
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.19.1.0 — automated matches

Domain ID domain_id	d3c5jb2
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)

CATH v4.4 (4 domains)

Domain ID domain_id	3c5jA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

Domain ID domain_id	3c5jA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3c5jB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily	10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1

Domain ID domain_id	3c5jB02
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	83.380 Å
Unit-cell length b length_b	83.380 Å
Unit-cell length c length_c	132.910 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 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	41.690 Å
R factor r_factor	—
R_work r_work	0.2020
R_free r_free	0.2270

Crystal structure of HLA DR52c

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

HLA class II histocompatibility antigen, DR alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

MHC class II antigen

State in the Current Structure

Other States of the Same Protein in the Database

Elongation factor 1-alpha 2

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

3c5j__assembly_2__model_1

3c5j__assembly_2__model_1 | I(q)

3c5j__assembly_2__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of HLA DR52c

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

HLA class II histocompatibility antigen, DR 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

MHC class II 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

Elongation factor 1-alpha 2

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

3c5j__assembly_2__model_1

3c5j__assembly_2__model_1 | I(q)

3c5j__assembly_2__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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)