3oxs

Crystal Structure of HLA A*02:07 Bound to HBV Core 18-27

Method: X-RAY DIFFRACTION Dmax: 74.7 Å Quality: EXCELLENT

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

MHC class I antigen

Homo sapiens

UniProt Q861F6

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 25–299 Fragment:UNP RESIDUES 25-299 Beta-2-microglobulin × 1 (P61769) 10mer peptide from Pre-core-protein × 1 (Q9YJW5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;298 K;0.1M sodium acetate tridydrate pH 4.6, 8% w/v polyethylene 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.75 Å R-free 0.207

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 Q861F6_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–275; UniProt 25–299

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 (Q861F6) 10mer peptide from Pre-core-protein × 1 (Q9YJW5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;298 K;0.1M sodium acetate tridydrate pH 4.6, 8% w/v polyethylene 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.75 Å R-free 0.207

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 1998 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 2–100; UniProt 21–119

10mer peptide from Pre-core-protein

OrganismNot specified

UniProt Q9YJW5

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 C; UniProt 47–56 Not recorded MHC class I antigen × 1 (Q861F6) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;298 K;0.1M sodium acetate tridydrate pH 4.6, 8% w/v polyethylene 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 1.75 Å R-free 0.207

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.

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9YJW5_HBV
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 47–56

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 3oxs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3oxs
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3oxs
Deposition date deposition_date2010-09-22
Structure title titleCrystal Structure of HLA A*02:07 Bound to HBV Core 18-27
Keywords keywords;Protein-Peptide Complex, Host-virus interaction, Immunogenicity, Therapeutic Design, TCR Recognition, Helix, Beta-sheet, Antigen Presentation, Peptide Binding, Cell Surface, 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_guinier24.10
Radius of gyration Rg (electron density) rg_electron22.90
Forward intensity I(0) i036246700.00
Molecular weight molecular_weight44756.0 kDa
Excluded volume excluded_volume55199 ų
Envelope volume envelope_volume67469 ų
Hydration-shell volume shell_volume24633 ų
Envelope diameter envelope_diameter77.9
Shell Rg shell_rg29.69
Envelope Rg envelope_rg22.99
Shape Rg shape_rg22.88
Total Rg total_rg23.75
Total atoms total_atoms3161
Residues n_residues385
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 dmax74.7
Rg (real space) rg_real24.03
Rg uncertainty (real space) rg_real_error0.45
I(0) (real space) i0_real3.6250e+07
I(0) uncertainty (real space) i0_real_error4.7240e+05
Rg (reciprocal space) rg_reciprocal24.05
I(0) (reciprocal space) i0_reciprocal36250000.0000
Solution quality estimate total_estimate0.9126
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.4
Skewness Skewness skewness0.235
Kurtosis Kurtosis kurtosis-0.483
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8960000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.996

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3oxsb1
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_idd3oxsb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id3oxsA01
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_id3oxsA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3oxsB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)