9wvf

Crystal structure of HLA-A*11:01 in complex with KRAS G12S 10-mer peptide (VVVGASGVGK)

Method: X-RAY DIFFRACTION Dmax: 120.9 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A alpha chain

Homo sapiens

UniProt P04439

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 Not recorded Beta-2-microglobulin × 1 (P61769) VAL-VAL-VAL-GLY-ALA-SER-GLY-VAL-GLY-LYS × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate Resolution 2.80 Å R-free 0.291
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) VAL-VAL-VAL-GLY-ALA-SER-GLY-VAL-GLY-LYS × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate Resolution 2.80 Å R-free 0.291
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain G; UniProt 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) VAL-VAL-VAL-GLY-ALA-SER-GLY-VAL-GLY-LYS × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate Resolution 2.80 Å R-free 0.291
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain J; UniProt 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) VAL-VAL-VAL-GLY-ALA-SER-GLY-VAL-GLY-LYS × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate Resolution 2.80 Å R-free 0.291

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.

53 other PDB entries and 75 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HLAA_HUMAN
Isoform P04439-2
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–276; UniProt 25–299 Author chain D; PDBConstruct 2–276; UniProt 25–299 Author chain G; PDBConstruct 2–276; UniProt 25–299 Author chain J; PDBConstruct 2–276; 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 HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) VAL-VAL-VAL-GLY-ALA-SER-GLY-VAL-GLY-LYS × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate Resolution 2.80 Å R-free 0.291
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) VAL-VAL-VAL-GLY-ALA-SER-GLY-VAL-GLY-LYS × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate Resolution 2.80 Å R-free 0.291
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) VAL-VAL-VAL-GLY-ALA-SER-GLY-VAL-GLY-LYS × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate Resolution 2.80 Å R-free 0.291
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain K; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A alpha chain × 1 (P04439) VAL-VAL-VAL-GLY-ALA-SER-GLY-VAL-GLY-LYS × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;291 K;29% PEG3350,0.1M Bis-Tris,PH5.2,0.2M Lithium sulfate Resolution 2.80 Å R-free 0.291

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 1995 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 Author chain E; PDBConstruct 2–100; UniProt 21–119 Author chain H; PDBConstruct 2–100; UniProt 21–119 Author chain K; PDBConstruct 2–100; 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 9wvf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9wvf
Deposition date deposition_date2025-09-19
Structure title titleCrystal structure of HLA-A*11:01 in complex with KRAS G12S 10-mer peptide (VVVGASGVGK)
Keywords keywordsComplex, 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_guinier39.04
Radius of gyration Rg (electron density) rg_electron38.21
Forward intensity I(0) i0511692000.00
Molecular weight molecular_weight176610.0 kDa
Excluded volume excluded_volume217480 ų
Envelope volume envelope_volume298190 ų
Hydration-shell volume shell_volume63978 ų
Envelope diameter envelope_diameter129.0
Shell Rg shell_rg45.10
Envelope Rg envelope_rg37.39
Shape Rg shape_rg38.21
Total Rg total_rg38.62
Total atoms total_atoms12472
Residues n_residues1536
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 dmax120.9
Rg (real space) rg_real38.80
Rg uncertainty (real space) rg_real_error0.73
I(0) (real space) i0_real5.1170e+08
I(0) uncertainty (real space) i0_real_error8.8050e+06
Rg (reciprocal space) rg_reciprocal38.95
I(0) (reciprocal space) i0_reciprocal511800000.0000
Solution quality estimate total_estimate0.8980
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.4
Skewness Skewness skewness0.152
Kurtosis Kurtosis kurtosis-0.457
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha50270000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.897

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)