SAXSdb — 1k2d

▼

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

H-2 class II histocompatibility antigen, A-U alpha chain

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–179	Fragment：EXTRACELLULAR ALPHA-1 AND ALPHA-2 DOMAINS	H-2 class II histocompatibility antigen, A-U beta chain × 1 （P06344） Myelin Basic Protein peptide with 8 residue linker peptide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；296 K；MPEG 5000, sodium chloride, citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 2.20 Å R-free 0.276

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1K2D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U3H Crystal structure of mouse TCR 172.10 complexed with MHC class II I-Au molecule at 2.4 A Deposited 2004-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–179（179 aa） Fragment：extracellular alpha-1, extracellular alpha-2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；21% PEG 3350, 0.1M Hepes and 0.2M LiSO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.42 Å R-free 0.274
1U3H Crystal structure of mouse TCR 172.10 complexed with MHC class II I-Au molecule at 2.4 A Deposited 2004-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 1–179（179 aa） Fragment：extracellular alpha-1, extracellular alpha-2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；21% PEG 3350, 0.1M Hepes and 0.2M LiSO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.42 Å R-free 0.274
2P24 I-Au/MBP125-135 Deposited 2007-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–190（190 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291.15 K；0.1 M NaOAc, 25% (w/v) PEG 1000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.15 Å R-free 0.260
2PXY Crystal structures of immune receptor complexes Deposited 2007-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–178（178 aa） Fragment：extracellular alpha-1, extracellular alpha-2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.2M Potassium sodium tartrate tetrahydrate, 0.1M succinic acid (pH7.0), 16% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.23 Å R-free 0.253
2Z31 Crystal structure of immune receptor complex Deposited 2007-05-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–178（178 aa） Fragment：extracellular alpha-1 and extracellular alpha-2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.2M patassium sodium tartrate tetrahydrate, 0.1M succinic acid, 16% polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.70 Å R-free 0.287

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HA2U_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–189； UniProt 1–179

H-2 class II histocompatibility antigen, A-U beta chain

Mus musculus

UniProt P06344

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 28–216	Fragment：EXTRACELLULAR BETA-1 AND BETA-2 DOMAINS	H-2 class II histocompatibility antigen, A-U alpha chain × 1 （P14438） Myelin Basic Protein peptide with 8 residue linker peptide × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；296 K；MPEG 5000, sodium chloride, citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 2.20 Å R-free 0.276

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1K2D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U3H Crystal structure of mouse TCR 172.10 complexed with MHC class II I-Au molecule at 2.4 A Deposited 2004-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 28–216（189 aa） Fragment：extracellular beta-1, extracellular beta-2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；21% PEG 3350, 0.1M Hepes and 0.2M LiSO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.42 Å R-free 0.274
1U3H Crystal structure of mouse TCR 172.10 complexed with MHC class II I-Au molecule at 2.4 A Deposited 2004-07-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 28–216（189 aa） Fragment：extracellular beta-1, extracellular beta-2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；21% PEG 3350, 0.1M Hepes and 0.2M LiSO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.42 Å R-free 0.274
2P24 I-Au/MBP125-135 Deposited 2007-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–224（197 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291.15 K；0.1 M NaOAc, 25% (w/v) PEG 1000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.15 Å R-free 0.260
2PXY Crystal structures of immune receptor complexes Deposited 2007-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 29–217（189 aa） Fragment：extracellular beta-1, extracellular beta-2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.2M Potassium sodium tartrate tetrahydrate, 0.1M succinic acid (pH7.0), 16% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.23 Å R-free 0.253
2Z31 Crystal structure of immune receptor complex Deposited 2007-05-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 28–216（189 aa） Fragment：extracellular beta-1 and extracellular beta-2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.2M patassium sodium tartrate tetrahydrate, 0.1M succinic acid, 16% polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 2.70 Å R-free 0.287

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HB2U_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–189； UniProt 28–216

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1k2d
Deposition date deposition_date	2001-09-26
Structure title title	Crystal structure of the autoimmune MHC class II I-Au complexed with myelin basic protein 1-11 at 2.2A
Keywords keywords	;MHC class II, I-Au, H-2u, autoimmune disease, unique register, experimental autoimmune encephalomyelitis, myelin basic protein, IMMUNE SYSTEM ;; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.94 Å
Radius of gyration Rg (electron density) rg_electron	23.94 Å
Forward intensity I(0) i0	33543500.00
Molecular weight molecular_weight	44487.0 kDa
Excluded volume excluded_volume	55523 Å³
Envelope volume envelope_volume	67783 Å³
Hydration-shell volume shell_volume	24126 Å³
Envelope diameter envelope_diameter	86.1 Å
Shell Rg shell_rg	30.37 Å
Envelope Rg envelope_rg	24.21 Å
Shape Rg shape_rg	23.90 Å
Total Rg total_rg	24.84 Å
Total atoms total_atoms	3147
Residues n_residues	377
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	85.5 Å
Rg (real space) rg_real	25.00 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	3.3540e+07
I(0) uncertainty (real space) i0_real_error	5.2010e+05
Rg (reciprocal space) rg_reciprocal	24.99 Å
I(0) (reciprocal space) i0_reciprocal	33540000.0000
Solution quality estimate total_estimate	0.7994
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.397
Kurtosis Kurtosis kurtosis	-0.307
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7157000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	H-2 class II histocompatibility antigen, A-U alpha chain
Molecular weight formula_weight	21468.8 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	3597

HSRGEDDIEADHVGSYGIVVYQSPGDIGQYTFEFDGDELFYVDLDKKETIWMLPEFAQLRSFDPQGGLQNIATGKHNLGVLTKRSNSTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVADGVYETSFFVNRDYSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEPE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	H-2 class II histocompatibility antigen, A-U beta chain
Molecular weight formula_weight	22495.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GDSERHFVVQFQPFCYFTNGTQRIRYVTRYIYNREEYLRFDSDVGEYRAVTELGRPDAEYYNKQYLERTRAELDTVCRYNYEETEVPTSLRRLEQPNVVISLSRTEALNHHNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPRRGEVYTCHVEHPSLKSPITVEWRA

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Drosophila melanogaster

Entity 3 Entity 3 polymer

Description description	Myelin Basic Protein peptide with 8 residue linker peptide
Molecular weight formula_weight	2319.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

HSRGGASQYRPSQRHGTGSGSGS

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	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	450

▼

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1k2da1
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	d1k2da2
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	d1k2da3
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	d1k2db1
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	d1k2db2
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

CATH v4.4 (4 domains)

Domain ID domain_id	1k2dA01
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	1k2dA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1k2dB01
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	1k2dB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	99.150 Å
Unit-cell length b length_b	110.590 Å
Unit-cell length c length_c	94.840 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2490
R_work r_work	0.2480
R_free r_free	0.2760

fit	/app/data/saxs_computation/k2/1k2d/1k2d.fit
pddf	/app/data/pr_computation/k2/1k2d/1k2d.pr.out
profile	/app/data/saxs_computation/k2/1k2d/1k2d.dat

Crystal structure of the autoimmune MHC class II I-Au complexed with myelin basic protein 1-11 at 2.2A

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

H-2 class II histocompatibility antigen, A-U alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

H-2 class II histocompatibility antigen, A-U beta chain

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)