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5dmk

Crystal Structure of IAg7 in complex with RLGL-WE14

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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

Mus musculus

UniProt P04228

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein × 1 （Q31135） CITRATE ANION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein × 1 （Q31135） water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein × 1 （Q31135） CITRATE ANION × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein × 1 （Q31135） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1iao

1 assemblies

Homotetramer
1iao

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1es0 1f3j 2iad 2iad 3cup 3mbe 3mbe 5dmk 5dmk 5dmk 5dmk 6blq

21 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HA2D_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–173； UniProt 26–198 Author chain C； PDBConstruct 1–173； UniProt 26–198 Author chain E； PDBConstruct 1–173； UniProt 26–198 Author chain G； PDBConstruct 1–173； UniProt 26–198

beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein

Mus musculus

UniProt Q31135

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 H-2 class II histocompatibility antigen, A-D alpha chain × 1 （P04228） CITRATE ANION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 H-2 class II histocompatibility antigen, A-D alpha chain × 1 （P04228） water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 H-2 class II histocompatibility antigen, A-D alpha chain × 1 （P04228） CITRATE ANION × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 H-2 class II histocompatibility antigen, A-D alpha chain × 1 （P04228） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1f3j 3cup 3mbe 3mbe 5dmk 5dmk 5dmk 5dmk 6blq 6blr 6blx 6dfs

16 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q31135_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 28–212； UniProt 31–215 Author chain D； PDBConstruct 28–212； UniProt 31–215 Author chain F； PDBConstruct 28–212； UniProt 31–215 Author chain H； PDBConstruct 28–212； UniProt 31–215

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_id5dmk
Deposition date deposition_date2015-09-08
Structure title titleCrystal Structure of IAg7 in complex with RLGL-WE14
Keywords keywordsChromogranin A, Type I Diabetes, T cell, fusion protein, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-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.

5dmk__assembly_1__model_1

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

Download this curve (.dat)

5dmk__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

5dmk__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）24.20 Å
Rg (electron density)23.32 Å
Total Rg24.19 Å
Atom count2973
Residues361
Excluded volume52425 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5dmk__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5dmk__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5dmk__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5dmk__assembly_4__model_1 dimeric （2） 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)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd5dmka1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd5dmka2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd5dmkc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd5dmkc2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd5dmke1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd5dmke2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd5dmkg1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd5dmkg2
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (16 domains)

Domain ID domain_id5dmkA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5dmkA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5dmkB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5dmkB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5dmkC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5dmkC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5dmkD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5dmkD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5dmkE01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5dmkE02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5dmkF01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5dmkF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5dmkG01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5dmkG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5dmkH01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id5dmkH02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)