7ow3

Crystal structure of HLA-A*11:01 in complex with KRAS peptide (VVVGAGGVGK)

Method: X-RAY DIFFRACTION Dmax: 136.3 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt A0A583ZB34

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) KRAS peptide (VVVGAGGVGK) × 1 (P01111) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260
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) KRAS peptide (VVVGAGGVGK) × 1 (P01111) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260
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) KRAS peptide (VVVGAGGVGK) × 1 (P01111) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260
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) KRAS peptide (VVVGAGGVGK) × 1 (P01111) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260

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.

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A583ZB34_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–275; UniProt 25–299 Author chain D; PDBConstruct 1–275; UniProt 25–299 Author chain G; PDBConstruct 1–275; UniProt 25–299 Author chain J; 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 (A0A583ZB34) KRAS peptide (VVVGAGGVGK) × 1 (P01111) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Not recorded MHC class I antigen × 1 (A0A583ZB34) KRAS peptide (VVVGAGGVGK) × 1 (P01111) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain H; UniProt 21–119 Not recorded MHC class I antigen × 1 (A0A583ZB34) KRAS peptide (VVVGAGGVGK) × 1 (P01111) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain K; UniProt 21–119 Not recorded MHC class I antigen × 1 (A0A583ZB34) KRAS peptide (VVVGAGGVGK) × 1 (P01111) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260

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

KRAS peptide (VVVGAGGVGK)

OrganismNot specified

UniProt P01111

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 7–16 Not recorded MHC class I antigen × 1 (A0A583ZB34) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 7–16 Not recorded MHC class I antigen × 1 (A0A583ZB34) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260
3 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain I; UniProt 7–16 Not recorded MHC class I antigen × 1 (A0A583ZB34) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260
4 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain L; UniProt 7–16 Not recorded MHC class I antigen × 1 (A0A583ZB34) Beta-2-microglobulin × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;293 K;0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6, 25% PEG 4000 Resolution 2.46 Å R-free 0.260

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.

33 other PDB entries and 59 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RASN_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 7–16 Author chain F; PDBConstruct 1–10; UniProt 7–16 Author chain I; PDBConstruct 1–10; UniProt 7–16 Author chain L; PDBConstruct 1–10; UniProt 7–16

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 7ow3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7ow3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7ow3
Deposition date deposition_date2021-06-16
Structure title titleCrystal structure of HLA-A*11:01 in complex with KRAS peptide (VVVGAGGVGK)
Keywords keywordsHLA, KRAS, 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_guinier41.05
Radius of gyration Rg (electron density) rg_electron40.53
Forward intensity I(0) i0512831000.00
Molecular weight molecular_weight177360.0 kDa
Excluded volume excluded_volume218390 ų
Envelope volume envelope_volume299110 ų
Hydration-shell volume shell_volume61908 ų
Envelope diameter envelope_diameter140.2
Shell Rg shell_rg45.53
Envelope Rg envelope_rg40.19
Shape Rg shape_rg40.50
Total Rg total_rg40.89
Total atoms total_atoms12518
Residues n_residues1530
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 dmax136.3
Rg (real space) rg_real41.05
Rg uncertainty (real space) rg_real_error1.07
I(0) (real space) i0_real5.1280e+08
I(0) uncertainty (real space) i0_real_error9.1320e+06
Rg (reciprocal space) rg_reciprocal41.05
I(0) (reciprocal space) i0_reciprocal512800000.0000
Solution quality estimate total_estimate0.8837
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.6
Skewness Skewness skewness0.340
Kurtosis Kurtosis kurtosis-0.381
Angular range angular_range— – 0.1900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha58510000.0000
Real-space data points n_real_points39
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.849

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id7ow3A01
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_id7ow3A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ow3D01
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_id7ow3D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ow3G01
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_id7ow3G02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7ow3J01
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_id7ow3J02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)