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5wli

Crystal Structure of H-2Db with the GAP501 peptide (SQL)

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

H-2 class I histocompatibility antigen, D-B alpha chain

Mus musculus

UniProt P01899

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Beta-2-microglobulin × 1 （P01887） GAP50 peptide × 1 （A0A0Y9W4B5） PHOSPHATE ION × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Beta-2-microglobulin × 1 （P01887） GAP50 peptide × 1 （A0A0Y9W4B5） water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Beta-2-microglobulin × 1 （P01887） GAP50 peptide × 1 （A0A0Y9W4B5） PHOSPHATE ION × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Beta-2-microglobulin × 1 （P01887） GAP50 peptide × 1 （A0A0Y9W4B5） PHOSPHATE ION × 1 water × 3 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
1bz9 1bz9 1ce6 1ffn 1ffn 1ffo 1ffo 1ffp 1ffp 1fg2 1fg2 1fg2

203 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name HA11_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–278； UniProt 25–302 Author chain D； PDBConstruct 1–278； UniProt 25–302 Author chain G； PDBConstruct 1–278； UniProt 25–302 Author chain J； PDBConstruct 1–278； UniProt 25–302

Beta-2-microglobulin

Mus musculus

UniProt P01887

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） GAP50 peptide × 1 （A0A0Y9W4B5） PHOSPHATE ION × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） GAP50 peptide × 1 （A0A0Y9W4B5） water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） GAP50 peptide × 1 （A0A0Y9W4B5） PHOSPHATE ION × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） GAP50 peptide × 1 （A0A0Y9W4B5） PHOSPHATE ION × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6i8c

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1bii 1bqh 1bqh 1bz9 1bz9 1cd1 1cd1 1ddh 1ffn 1ffn 1ffo 1ffo

483 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name B2MG_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–99； UniProt 21–119 Author chain E； PDBConstruct 1–99； UniProt 21–119 Author chain H； PDBConstruct 1–99； UniProt 21–119 Author chain K； PDBConstruct 1–99； UniProt 21–119

GAP50 peptide

OrganismNot specified

UniProt A0A0Y9W4B5

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） PHOSPHATE ION × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） water × 3 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） PHOSPHATE ION × 1 water × 3 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 H-2 class I histocompatibility antigen, D-B alpha chain × 1 （P01899） Beta-2-microglobulin × 1 （P01887） PHOSPHATE ION × 1 water × 3 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
5wlg 5wlg 5wli 5wli 5wli 5wli

6 assemblies

View Construct and Data Evidence
UniProt name A0A0Y9W4B5_PLABE
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–9； UniProt 40–48 Author chain F； PDBConstruct 1–9； UniProt 40–48 Author chain I； PDBConstruct 1–9； UniProt 40–48 Author chain L； PDBConstruct 1–9； UniProt 40–48

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_id5wli
Deposition date deposition_date2017-07-27
Structure title titleCrystal Structure of H-2Db with the GAP501 peptide (SQL)
Keywords keywordsH-2Db, malaria, GAP50, Immune response gene, TCR, T cell, Vb8.1, 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.

5wli__assembly_1__model_1

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

Download this curve (.dat)

5wli__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.

5wli__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）24.06 Å
Rg (electron density)23.16 Å
Total Rg24.01 Å
Atom count3153
Residues383
Excluded volume55416 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5wli__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5wli__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 5wli__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 5wli__assembly_4__model_1 trimeric （3） 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)

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id5wliA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5wliA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wliB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wliD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5wliD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wliE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wliG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5wliG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wliH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wliJ01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id5wliJ02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5wliK00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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7. Citations (1)