1lo5

Crystal structure of the D227A variant of Staphylococcal enterotoxin A in complex with human MHC class II

Method: X-RAY DIFFRACTION

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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 4	HLA class II histocompatibility antigen, DR-1 beta chain × 1 （P04229） Hemagglutinin peptide × 1 enterotoxin A × 1 （P0A0L2） water × 3	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 1–182； UniProt 26–207

HLA class II histocompatibility antigen, DR-1 beta chain

Homo sapiens

UniProt P04229

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	HLA class II histocompatibility antigen, DR alpha chain × 1 （P01903） Hemagglutinin peptide × 1 enterotoxin A × 1 （P0A0L2） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	2B11_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–190； UniProt 30–219

enterotoxin A

Staphylococcus aureus

UniProt P0A0L2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	HLA class II histocompatibility antigen, DR alpha chain × 1 （P01903） HLA class II histocompatibility antigen, DR-1 beta chain × 1 （P04229） Hemagglutinin peptide × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ETXA_STAAU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–233； UniProt 25–257

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	1lo5
Deposition date deposition_date	2002-05-06
Structure title title	Crystal structure of the D227A variant of Staphylococcal enterotoxin A in complex with human MHC class II
Keywords keywords	PROTEIN-PROTEIN COMPLEX, IMMUNE SYSTEM-Toxin COMPLEX; IMMUNE SYSTEM/Toxin
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.

1lo5__assembly_1__model_1

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

Download this curve (.dat)

1lo5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1lo5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.06 Å
Rg (electron density)	30.45 Å
Total Rg	31.08 Å
Atom count	5032
Residues	613
Excluded volume	89045 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1lo5__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	HLA class II histocompatibility antigen, DR alpha chain
Molecular weight formula_weight	21155.9 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	5055

IKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDA

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	HLA class II histocompatibility antigen, DR-1 beta chain
Molecular weight formula_weight	22080.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA

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	Hemagglutinin peptide
Molecular weight formula_weight	1506.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

PKYVKQNTLKLAT

Entity 4 Entity 4 polymer

Description description	enterotoxin A
Molecular weight formula_weight	27086.3 kDa
Mutation mutation	D227A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

SEKSEEINEKDLRKKSELQGTALGNLKQIYYYNEKAKTENKESHDQFLQHTILFKGFFTDHSWYNDLLVDFDSKDIVDKYKGKKVDLYGAYYGYQCAGGTPNKTACMYGGVTLHDNNRLTEEKKVPINLWLDGKQNTVPLETVKTNKKNVTVQELDLQARRYLQEKYNLYNSDVFDGKVQRGLIVFHTSTEPSVNYDLFGAQGQYSNTLLRIYRDNKTINSENMHIAIYLYTS

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	23

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1lo5a1
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	d1lo5a2
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	d1lo5b1
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	d1lo5b2
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	d1lo5d1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.2 — Bacterial enterotoxins
Family Family family	b.40.2.2 — Superantigen toxins, N-terminal domain

Domain ID domain_id	d1lo5d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.6 — Superantigen toxins, C-terminal domain
Family Family family	d.15.6.1 — Superantigen toxins, C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1lo5A01
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	1lo5A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1lo5B01
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	1lo5B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1lo5D01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	110 —

Domain ID domain_id	1lo5D02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	120 —

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Unit-cell length a length_a	52.008 Å
Unit-cell length b length_b	75.792 Å
Unit-cell length c length_c	198.082 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2450
R_work r_work	0.2450
R_free r_free	0.3390

Crystal structure of the D227A variant of Staphylococcal enterotoxin A in complex with human MHC class II

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

HLA class II histocompatibility antigen, DR-1 beta chain

State in the Current Structure

Other States of the Same Protein in the Database

enterotoxin A

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

1lo5__assembly_1__model_1

1lo5__assembly_1__model_1 | I(q)

1lo5__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 (5)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the D227A variant of Staphylococcal enterotoxin A in complex with human MHC class II

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

HLA class II histocompatibility antigen, DR-1 beta 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

enterotoxin A

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

1lo5__assembly_1__model_1

1lo5__assembly_1__model_1 | I(q)

1lo5__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 (5)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)