5ujt

Crystal structure of human HLA-DQ8 in complex with insulin mimotope binding in register 3

Method: X-RAY DIFFRACTION D_max: 109.8 Å Quality: GOOD

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

MHC class II antigen

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 23–207	Not recorded	MHC class II HLA-DQ-beta-1 × 1 （O19707） insulin mimotope × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；278 K；15% PEG3350, 100mM Tacsimate	Resolution 1.94 Å R-free 0.238
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 23–207	Not recorded	MHC class II HLA-DQ-beta-1 × 1 （O19707） insulin mimotope × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；278 K；15% PEG3350, 100mM Tacsimate	Resolution 1.94 Å R-free 0.238
3	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 23–207	Not recorded	MHC class II HLA-DQ-beta-1 × 1 （O19707） insulin mimotope × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；278 K；15% PEG3350, 100mM Tacsimate	Resolution 1.94 Å R-free 0.238

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q5Y7C3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–185； UniProt 23–207 Author chain D； PDBConstruct 1–185； UniProt 23–207 Author chain G； PDBConstruct 1–185； UniProt 23–207

MHC class II HLA-DQ-beta-1

Homo sapiens

UniProt O19707

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 3–191	Not recorded	MHC class II antigen × 1 （Q5Y7C3） insulin mimotope × 1 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；278 K；15% PEG3350, 100mM Tacsimate	Resolution 1.94 Å R-free 0.238
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 3–191	Not recorded	MHC class II antigen × 1 （Q5Y7C3） insulin mimotope × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；278 K；15% PEG3350, 100mM Tacsimate	Resolution 1.94 Å R-free 0.238
3	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain H； UniProt 3–191	Not recorded	MHC class II antigen × 1 （Q5Y7C3） insulin mimotope × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.5；278 K；15% PEG3350, 100mM Tacsimate	Resolution 1.94 Å R-free 0.238

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5UJT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4Z7U S13 complex Deposited 2015-04-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa） Fragment：UNP residues 1-192	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；140 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 7.5, 15% PEG8000	Resolution 2.70 Å R-free 0.220
4Z7U S13 complex Deposited 2015-04-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–192（192 aa） Fragment：UNP residues 1-192	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；140 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 7.5, 15% PEG8000	Resolution 2.70 Å R-free 0.220
4Z7V L3-12 complex Deposited 2015-04-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa） Fragment：UNP residues 1-192	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；80 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 6.5, 16% PEG8000	Resolution 2.65 Å R-free 0.226
4Z7V L3-12 complex Deposited 2015-04-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–192（192 aa） Fragment：UNP residues 1-192	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；80 mM Na-acetate, 0.1 M Bis-Tris-Propane pH 6.5, 16% PEG8000	Resolution 2.65 Å R-free 0.226
4Z7W T316 complex Deposited 2015-04-08	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa） Fragment：UNP residues 1-192	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.32 M (NH4)2SO4, 0.1 M HEPES pH 7.8, 20% PEG3350	Resolution 2.89 Å R-free 0.247
4Z7W T316 complex Deposited 2015-04-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–192（192 aa） Fragment：UNP residues 1-192	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.32 M (NH4)2SO4, 0.1 M HEPES pH 7.8, 20% PEG3350	Resolution 2.89 Å R-free 0.247
5KSA Bel602-DQ8.5-glia-gamma1 complex Deposited 2016-07-08	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 B 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Ca-Acetate, 21 % PEG3350, Tris pH 8.0	Resolution 2.00 Å R-free 0.206
5KSB T15-DQ8.5-glia-gamma1 complex Deposited 2016-07-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；8% Tacsimate pH 7.5, 20% PEG3350	Resolution 2.90 Å R-free 0.254
5KSB T15-DQ8.5-glia-gamma1 complex Deposited 2016-07-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；8% Tacsimate pH 7.5, 20% PEG3350	Resolution 2.90 Å R-free 0.254
6XCO Immune receptor complex Deposited 2020-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 6 CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293.15 K；0.1 M calcium acetate, 0.1 M sodium cacodylate pH 5.5, 13% polyethylene glycol (PEG) 20,000	Resolution 2.90 Å R-free 0.247
6XCP Immune receptor complex Deposited 2020-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；13% PEG 8000, 0.2M Potassium dihydrogen phosphate	Resolution 3.30 Å R-free 0.268
8VCX Human TCR A2.13 in complex with DQ8-InsCpep Deposited 2023-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa）	Not recorded	PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M Potassium sodium tartrate, 24% PEG 3350	Resolution 2.59 Å R-free 0.238
8VCY Human TCR A2.13 in complex with DQ8-InsC8-15NPY Deposited 2023-12-14	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 B 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 5 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M Potassium sodium tartrate, 14% PEG 20,000 with seeding C8 silver bullet (Hampton Research)	Resolution 2.60 Å R-free 0.225
8VD0 Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2 Deposited 2023-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 4 PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M K Na tartrate, 15% w/v PEG 20,000 with seeding and additive C8 silver bullet	Resolution 2.40 Å R-free 0.220
8VD0 Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP2 Deposited 2023-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 8 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M K Na tartrate, 15% w/v PEG 20,000 with seeding and additive C8 silver bullet	Resolution 2.40 Å R-free 0.220
8VD2 Human TCR ET650-4 in complex with DQ8-InsC8-15-IAPP1 Deposited 2023-12-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M potassium dihydrogen phosphate (KH2PO4), 15% w/v PEG 20,000 with seeding and additive 30 mM MnCl2	Resolution 2.90 Å R-free 0.259
8VDD Crystal structure of Proinsulin C-peptide bound to HLA-DQ8 Deposited 2023-12-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M K Na tartrate, 14% w/v PEG 20,000 with seeding and additive C8 silver bullet	Resolution 2.60 Å R-free 0.280
8VDU Crystal structure of hybrid insulin peptide (InsC8-15-IAPP74-80) bound to HLA-DQ8 Deposited 2023-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 1–192（192 aa） Chain E 1–192（192 aa） Chain H 1–192（192 aa） Chain K 1–192（192 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；0.2 M Monopotassium phosphate, 17% PEG 8K	Resolution 3.50 Å R-free 0.246

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	O19707_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–189； UniProt 3–191 Author chain E； PDBConstruct 1–189； UniProt 3–191 Author chain H； PDBConstruct 1–189； UniProt 3–191

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ujt
Deposition date deposition_date	2017-01-18
Structure title title	Crystal structure of human HLA-DQ8 in complex with insulin mimotope binding in register 3
Keywords keywords	INSULIN, TYPE I DIABETES, T CELL, AUTOIMMUNE DISEASE, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	35.97 Å
Radius of gyration Rg (electron density) rg_electron	35.26 Å
Forward intensity I(0) i0	272199000.00
Molecular weight molecular_weight	132800.0 kDa
Excluded volume excluded_volume	165750 Å³
Envelope volume envelope_volume	220640 Å³
Hydration-shell volume shell_volume	51904 Å³
Envelope diameter envelope_diameter	113.2 Å
Shell Rg shell_rg	42.25 Å
Envelope Rg envelope_rg	34.64 Å
Shape Rg shape_rg	35.25 Å
Total Rg total_rg	35.77 Å
Total atoms total_atoms	9398
Residues n_residues	1141
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

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

Maximum dimension Dmax dmax	109.8 Å
Rg (real space) rg_real	35.86 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	2.7220e+08
I(0) uncertainty (real space) i0_real_error	4.7080e+06
Rg (reciprocal space) rg_reciprocal	35.93 Å
I(0) (reciprocal space) i0_reciprocal	272200000.0000
Solution quality estimate total_estimate	0.8983
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.4 Å
Skewness Skewness skewness	0.201
Kurtosis Kurtosis kurtosis	-0.608
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30190000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.767

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	MHC class II antigen
Molecular weight formula_weight	21138.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G
Atom count atom_count	10048

GEDIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNCVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSDDEIYDCKVEHWGLDEPLLKHWEPE

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	MHC class II HLA-DQ-beta-1
Molecular weight formula_weight	22246.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

SPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	insulin mimotope
Molecular weight formula_weight	1581.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

GVEELYLVAGEEGCGG

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 4 Entity 4 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	627.6 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 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 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	645

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d5ujta1
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	d5ujta2
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	d5ujtb1
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	d5ujtb2
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	d5ujtd1
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	d5ujtd2
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	d5ujte1
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	d5ujte2
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	d5ujtg1
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	d5ujtg2
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	d5ujth1
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	d5ujth2
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 (12 domains)

Domain ID domain_id	5ujtA01
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	5ujtA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ujtB01
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	5ujtB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ujtD01
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	5ujtD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ujtE01
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	5ujtE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ujtG01
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	5ujtG02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ujtH01
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	5ujtH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	72.038 Å
Unit-cell length b length_b	138.767 Å
Unit-cell length c length_c	159.735 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	12

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

Resolution resolution	1.940 Å
Low-resolution limit resolution_low	79.870 Å
R factor r_factor	0.2100
R_work r_work	0.2090
R_free r_free	0.2380

fit	/app/data/saxs_computation/uj/5ujt/5ujt.fit
pddf	/app/data/pr_computation/uj/5ujt/5ujt.pr.out
profile	/app/data/saxs_computation/uj/5ujt/5ujt.dat

Crystal structure of human HLA-DQ8 in complex with insulin mimotope binding in register 3

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

MHC class II antigen

State in the Current Structure

Other States of the Same Protein in the Database

MHC class II HLA-DQ-beta-1

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 (6)

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

来源 Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)