1d5x

X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH DIPEPTIDE MIMETIC AND SEB

Method: X-RAY DIFFRACTION Dmax: 104.7 Å Quality: GOOD

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

HLA CLASS II HISTOCOMPATIBILITY ANTIGEN

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 26–206 Fragment:DR ALPHA CHAIN, EXTRACELLULAR DOMAIN HLA CLASS II HISTOCOMPATIBILITY ANTIGEN × 1 (P13760) ENTEROTOXIN TYPE B × 1 (P01552) DIPEPTIDE MIMETIC INHIBITOR × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.45 Å R-free 0.268

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 HA2R_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–181; UniProt 26–206

HLA CLASS II HISTOCOMPATIBILITY ANTIGEN

Homo sapiens

UniProt P13760

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 30–221 Fragment:DR-4 BETA CHAIN, EXTRACELLULAR DOMAIN HLA CLASS II HISTOCOMPATIBILITY ANTIGEN × 1 (P01903) ENTEROTOXIN TYPE B × 1 (P01552) DIPEPTIDE MIMETIC INHIBITOR × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.45 Å R-free 0.268

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.

32 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HB2H_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–192; UniProt 30–221

ENTEROTOXIN TYPE B

OrganismNot specified

UniProt P01552

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 28–266 Not recorded HLA CLASS II HISTOCOMPATIBILITY ANTIGEN × 1 (P01903) HLA CLASS II HISTOCOMPATIBILITY ANTIGEN × 1 (P13760) DIPEPTIDE MIMETIC INHIBITOR × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.45 Å R-free 0.268

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.

22 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ETXB_STAAU
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; 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 1d5x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d5x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d5x
Deposition date deposition_date1999-10-12
Structure title titleX-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH DIPEPTIDE MIMETIC AND SEB
Keywords keywordsMHC CLASS II-SUPERANTIGEN COMPLEX, IMMUNE SYSTEM-PEPTIDE INHIBITOR COMPLEX, PEPTIDEOMIMETIC INHIBITOR; IMMUNE SYSTEM/PEPTIDE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.13
Radius of gyration Rg (electron density) rg_electron29.49
Forward intensity I(0) i076049100.00
Molecular weight molecular_weight69319.0 kDa
Excluded volume excluded_volume86835 ų
Envelope volume envelope_volume110780 ų
Hydration-shell volume shell_volume32136 ų
Envelope diameter envelope_diameter112.4
Shell Rg shell_rg35.76
Envelope Rg envelope_rg29.58
Shape Rg shape_rg29.44
Total Rg total_rg30.22
Total atoms total_atoms4900
Residues n_residues586
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 dmax104.7
Rg (real space) rg_real30.19
Rg uncertainty (real space) rg_real_error1.12
I(0) (real space) i0_real7.6050e+07
I(0) uncertainty (real space) i0_real_error1.2690e+06
Rg (reciprocal space) rg_reciprocal30.16
I(0) (reciprocal space) i0_reciprocal76050000.0000
Solution quality estimate total_estimate0.8750
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.6
Skewness Skewness skewness0.383
Kurtosis Kurtosis kurtosis-0.252
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11980000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.822; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.929; Smooth: 0.976

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_idd1d5xa1
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_idd1d5xa2
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_idd1d5xb1
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_idd1d5xb2
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_idd1d5xc1
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_idd1d5xc2
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_id1d5xA01
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_id1d5xA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1d5xB01
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_id1d5xB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1d5xC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily110
Domain ID domain_id1d5xC02
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)