1t5x

HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and the superantigen SEC3-3B2

Method: X-RAY DIFFRACTION Dmax: 104.9 Å Quality: GOOD

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 27–207 Fragment:Extracellular domain HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) 15-mer peptide fragment of Regulatory protein MIG1 × 1 (P27705) Enterotoxin type C-3 × 1 (P0A0L5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.4;277 K;PEG 4000, Ethylene Glycol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.50 Å R-free 0.241

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.

139 other PDB entries and 219 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 2DRA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–181; UniProt 27–207

HLA class II histocompatibility antigen, DRB1-1 beta chain

Homo sapiens

UniProt P04229

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 30–219 Fragment:Extracellular domain HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) 15-mer peptide fragment of Regulatory protein MIG1 × 1 (P27705) Enterotoxin type C-3 × 1 (P0A0L5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.4;277 K;PEG 4000, Ethylene Glycol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.50 Å R-free 0.241

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.

48 other PDB entries and 83 assemblies. Open the comparison page and filter oligomeric states

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

15-mer peptide fragment of Regulatory protein MIG1

OrganismNot specified

UniProt P27705

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 455–462 Fragment:Synthetic peptide HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) Enterotoxin type C-3 × 1 (P0A0L5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.4;277 K;PEG 4000, Ethylene Glycol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.50 Å R-free 0.241

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.

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MIG1_YEAST
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 8–15; UniProt 455–462

Enterotoxin type C-3

Staphylococcus aureus

UniProt P0A0L5

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 28–266 Fragment:SEC3 variant 3B2 Mutation:K43S, L45F, A46K, H47W HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) 15-mer peptide fragment of Regulatory protein MIG1 × 1 (P27705) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.4;277 K;PEG 4000, Ethylene Glycol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.50 Å R-free 0.241

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.

17 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ENTC3_STAAU
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–239; UniProt 28–266

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

SAXS profile for 1t5x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1t5x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1t5x
Deposition date deposition_date2004-05-05
Structure title titleHLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and the superantigen SEC3-3B2
Keywords keywordsMHC class II; major histocompatibiloty complex protein; HLA-DR1; superantigen; antigen; peptide, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.61
Radius of gyration Rg (electron density) rg_electron29.90
Forward intensity I(0) i081004600.00
Molecular weight molecular_weight70883.0 kDa
Excluded volume excluded_volume88498 ų
Envelope volume envelope_volume111700 ų
Hydration-shell volume shell_volume32169 ų
Envelope diameter envelope_diameter112.2
Shell Rg shell_rg35.85
Envelope Rg envelope_rg29.87
Shape Rg shape_rg29.87
Total Rg total_rg30.54
Total atoms total_atoms5005
Residues n_residues612
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax104.9
Rg (real space) rg_real30.69
Rg uncertainty (real space) rg_real_error0.96
I(0) (real space) i0_real8.1000e+07
I(0) uncertainty (real space) i0_real_error1.3900e+06
Rg (reciprocal space) rg_reciprocal30.66
I(0) (reciprocal space) i0_reciprocal81000000.0000
Solution quality estimate total_estimate0.8756
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.3
Skewness Skewness skewness0.399
Kurtosis Kurtosis kurtosis-0.233
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12310000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.921

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1t5xa1
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_idd1t5xa2
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_idd1t5xb1
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_idd1t5xb2
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_idd1t5xd1
Class classb — All beta proteins
Fold Fold foldb.40 — OB-fold
Superfamily Superfamily superfamilyb.40.2 — Bacterial enterotoxins
Family Family familyb.40.2.2 — Superantigen toxins, N-terminal domain
Domain ID domain_idd1t5xd2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.6 — Superantigen toxins, C-terminal domain
Family Family familyd.15.6.1 — Superantigen toxins, C-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id1t5xA01
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_id1t5xA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1t5xB01
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_id1t5xB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1t5xD01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id1t5xD02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily120

8. Citations (1)

9. Files and Curves (10)