9cwy

Crystal structure of HLA-A*03:02 in complex with a wild-type PIK3CA peptide

Method: X-RAY DIFFRACTION Dmax: 74.5 Å Quality: EXCELLENT

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

HLA class I histocompatibility antigen A alpha chain

Homo sapiens

UniProt C5IWY0

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 25–298 Not recorded Beta-2-microglobulin × 1 (P61769) wild-type PIK3CA peptide × 1 (P42336) ACT ACETATE ION × 2 FMT FORMIC ACID × 7 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277.15 K;12% w/v polyethylene glycol 3,350, 4% v/v Tacsimate (Hampton Research) Resolution 1.98 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.

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

View Construct and Data Evidence
UniProt name C5IWY0_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–274; UniProt 25–298

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 Fragment:UNP residues 21-119 HLA class I histocompatibility antigen A alpha chain × 1 (C5IWY0) wild-type PIK3CA peptide × 1 (P42336) ACT ACETATE ION × 2 FMT FORMIC ACID × 7 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277.15 K;12% w/v polyethylene glycol 3,350, 4% v/v Tacsimate (Hampton Research) Resolution 1.98 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.

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

wild-type PIK3CA peptide

OrganismNot specified

UniProt P42336

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 1046–1054 Not recorded HLA class I histocompatibility antigen A alpha chain × 1 (C5IWY0) Beta-2-microglobulin × 1 (P61769) ACT ACETATE ION × 2 FMT FORMIC ACID × 7 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;277.15 K;12% w/v polyethylene glycol 3,350, 4% v/v Tacsimate (Hampton Research) Resolution 1.98 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.

134 other PDB entries and 145 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PK3CA_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 1046–1054

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 9cwy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9cwy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9cwy
Deposition date deposition_date2024-07-30
最后修订 last_revision2026-02-04
Structure title titleCrystal structure of HLA-A*03:02 in complex with a wild-type PIK3CA peptide
Keywords keywordsPeptide-class I Major Histocompatibility Complex, pMHC, 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_guinier24.03
Radius of gyration Rg (electron density) rg_electron22.90
Forward intensity I(0) i037472100.00
Molecular weight molecular_weight44819.0 kDa
Excluded volume excluded_volume55046 ų
Envelope volume envelope_volume67681 ų
Hydration-shell volume shell_volume24776 ų
Envelope diameter envelope_diameter78.5
Shell Rg shell_rg29.58
Envelope Rg envelope_rg22.93
Shape Rg shape_rg22.87
Total Rg total_rg23.76
Total atoms total_atoms3163
Residues n_residues382
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 dmax74.5
Rg (real space) rg_real23.95
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real3.7470e+07
I(0) uncertainty (real space) i0_real_error5.0900e+05
Rg (reciprocal space) rg_reciprocal23.97
I(0) (reciprocal space) i0_reciprocal37470000.0000
Solution quality estimate total_estimate0.9106
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.3
Skewness Skewness skewness0.228
Kurtosis Kurtosis kurtosis-0.493
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9394000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.952; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)