2ipk

Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) and the Superantigen, SEC3 Variant 3B2

Method: X-RAY DIFFRACTION Dmax: 105.1 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 26–207 Fragment:Extracellular domain, residues 26-207 HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) × 1 Enterotoxin type C-3 × 1 (P0A0L3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.3;277 K;PEG 4000, Ethylene Glycol, Sodium Acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.30 Å R-free 0.224

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 2–183; UniProt 26–207

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, residues 30-219 HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) × 1 Enterotoxin type C-3 × 1 (P0A0L3) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.3;277 K;PEG 4000, Ethylene Glycol, Sodium Acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.30 Å R-free 0.224

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

Enterotoxin type C-3

Staphylococcus aureus subsp. aureus Mu50

UniProt P0A0L3

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:Residues 28-266 Mutation:K70S, L72F, A73K, H74W HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.3;277 K;PEG 4000, Ethylene Glycol, Sodium Acetate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.30 Å R-free 0.224

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 ENTC3_STAAM
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 2–240; 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 2ipk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ipk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ipk
Deposition date deposition_date2006-10-12
Structure title titleCrystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) and the Superantigen, SEC3 Variant 3B2
Keywords keywords;HLA, DR1, MHC, Major Histocompatibility Complex, Fluorogenic Probe, SEC3, 4-(N, N-dimethylamino)phthalimidoalanyl, DAPA, 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_guinier30.50
Radius of gyration Rg (electron density) rg_electron29.76
Forward intensity I(0) i082049400.00
Molecular weight molecular_weight71454.0 kDa
Excluded volume excluded_volume89264 ų
Envelope volume envelope_volume113090 ų
Hydration-shell volume shell_volume32594 ų
Envelope diameter envelope_diameter112.5
Shell Rg shell_rg35.88
Envelope Rg envelope_rg29.81
Shape Rg shape_rg29.73
Total Rg total_rg30.40
Total atoms total_atoms5045
Residues n_residues613
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 dmax105.1
Rg (real space) rg_real30.58
Rg uncertainty (real space) rg_real_error0.89
I(0) (real space) i0_real8.2050e+07
I(0) uncertainty (real space) i0_real_error1.2610e+06
Rg (reciprocal space) rg_reciprocal30.55
I(0) (reciprocal space) i0_reciprocal82050000.0000
Solution quality estimate total_estimate0.8733
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.4
Skewness Skewness skewness0.409
Kurtosis Kurtosis kurtosis-0.213
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12980000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.929

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_idd2ipka1
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_idd2ipka2
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_idd2ipkb1
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_idd2ipkb2
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_idd2ipkd1
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_idd2ipkd2
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_id2ipkA01
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_id2ipkA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ipkB01
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_id2ipkB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id2ipkD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily120
Domain ID domain_id2ipkD02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110

8. Citations (1)

9. Files and Curves (10)