6vqy

HLA-B*27:05 presenting an HIV-1 7mer peptide

Method: X-RAY DIFFRACTION Dmax: 107.3 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt O78189

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) 7-mer peptide × 1 ARG ARGININE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;30 %w/v Polyethylene Glycol Monomethyl Ether 5000, 0.2 M Ammonium Sulphate, 0.1 M MES pH 6.5 Resolution 2.57 Å R-free 0.238
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) 7-mer peptide × 1 ARG ARGININE × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;30 %w/v Polyethylene Glycol Monomethyl Ether 5000, 0.2 M Ammonium Sulphate, 0.1 M MES pH 6.5 Resolution 2.57 Å R-free 0.238

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.

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name O78189_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 25–300 Author chain C; PDBConstruct 1–276; UniProt 25–300

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded MHC class I antigen × 1 (O78189) 7-mer peptide × 1 ARG ARGININE × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;30 %w/v Polyethylene Glycol Monomethyl Ether 5000, 0.2 M Ammonium Sulphate, 0.1 M MES pH 6.5 Resolution 2.57 Å R-free 0.238
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 21–119 Not recorded MHC class I antigen × 1 (O78189) 7-mer peptide × 1 ARG ARGININE × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.5;277 K;30 %w/v Polyethylene Glycol Monomethyl Ether 5000, 0.2 M Ammonium Sulphate, 0.1 M MES pH 6.5 Resolution 2.57 Å R-free 0.238

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.

1313 other PDB entries and 1997 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–99; UniProt 21–119 Author chain D; PDBConstruct 1–99; UniProt 21–119

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 6vqy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6vqy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6vqy
Deposition date deposition_date2020-02-06
Structure title titleHLA-B*27:05 presenting an HIV-1 7mer peptide
Keywords keywordsHuman Leukocyte Antigen, Human Immunodeficiency Virus, 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_guinier32.79
Radius of gyration Rg (electron density) rg_electron32.02
Forward intensity I(0) i0135333000.00
Molecular weight molecular_weight89373.0 kDa
Excluded volume excluded_volume110300 ų
Envelope volume envelope_volume144000 ų
Hydration-shell volume shell_volume38059 ų
Envelope diameter envelope_diameter105.2
Shell Rg shell_rg38.50
Envelope Rg envelope_rg31.74
Shape Rg shape_rg32.00
Total Rg total_rg32.58
Total atoms total_atoms6315
Residues n_residues762
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 dmax107.3
Rg (real space) rg_real32.76
Rg uncertainty (real space) rg_real_error0.90
I(0) (real space) i0_real1.3530e+08
I(0) uncertainty (real space) i0_real_error2.2780e+06
Rg (reciprocal space) rg_reciprocal32.77
I(0) (reciprocal space) i0_reciprocal135300000.0000
Solution quality estimate total_estimate0.8998
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary105.1
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.547
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18080000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.936

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)