1qr1

POOR BINDING OF A HER-2/NEU EPITOPE (GP2) TO HLA-A2.1 IS DUE TO A LACK OF INTERACTIONS IN THE CENTER OF THE PEPTIDE

Method: X-RAY DIFFRACTION Dmax: 128.1 Å Quality: GOOD

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

HLA-A2.1 HEAVY CHAIN

Homo sapiens

UniProt P01892

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:RESIDUES 1-275 OF EXTRACELLULAR PORTION BETA-2 MICROGLOBULIN × 1 (P61769) GP2 PEPTIDE × 1 (P04626) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;14% PEG 6000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 2.40 Å R-free 0.284
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 25–299 Fragment:RESIDUES 1-275 OF EXTRACELLULAR PORTION BETA-2 MICROGLOBULIN × 1 (P61769) GP2 PEPTIDE × 1 (P04626) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;14% PEG 6000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 2.40 Å R-free 0.284

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.

271 other PDB entries and 464 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A02_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

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 Mutation:B2M HAS AN ADDED METHIONINE FOR BACTERIAL EXPRESSION HLA-A2.1 HEAVY CHAIN × 1 (P01892) GP2 PEPTIDE × 1 (P04626) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;14% PEG 6000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 2.40 Å R-free 0.284
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 21–119 Mutation:B2M HAS AN ADDED METHIONINE FOR BACTERIAL EXPRESSION HLA-A2.1 HEAVY CHAIN × 1 (P01892) GP2 PEPTIDE × 1 (P04626) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;14% PEG 6000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 2.40 Å R-free 0.284

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 1–100; UniProt 21–119 Author chain E; PDBConstruct 1–100; UniProt 21–119

GP2 PEPTIDE

OrganismNot specified

UniProt P04626

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 654–662 Not recorded HLA-A2.1 HEAVY CHAIN × 1 (P01892) BETA-2 MICROGLOBULIN × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;14% PEG 6000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 2.40 Å R-free 0.284
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 654–662 Not recorded HLA-A2.1 HEAVY CHAIN × 1 (P01892) BETA-2 MICROGLOBULIN × 1 (P61769) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;295 K;14% PEG 6000, 25 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K Resolution 2.40 Å R-free 0.284

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.

57 other PDB entries and 79 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ERBB2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 654–662 Author chain F; PDBConstruct 1–9; UniProt 654–662

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 1qr1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1qr1
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1qr1
Deposition date deposition_date1999-06-17
Structure title titlePOOR BINDING OF A HER-2/NEU EPITOPE (GP2) TO HLA-A2.1 IS DUE TO A LACK OF INTERACTIONS IN THE CENTER OF THE PEPTIDE
Keywords keywordsPEPTIDE-BINDING SUPERDOMAIN, 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_guinier40.64
Radius of gyration Rg (electron density) rg_electron40.57
Forward intensity I(0) i0128746000.00
Molecular weight molecular_weight89091.0 kDa
Excluded volume excluded_volume110010 ų
Envelope volume envelope_volume156100 ų
Hydration-shell volume shell_volume33297 ų
Envelope diameter envelope_diameter134.0
Shell Rg shell_rg43.93
Envelope Rg envelope_rg39.40
Shape Rg shape_rg40.57
Total Rg total_rg40.77
Total atoms total_atoms6292
Residues n_residues768
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 dmax128.1
Rg (real space) rg_real40.88
Rg uncertainty (real space) rg_real_error0.98
I(0) (real space) i0_real1.2870e+08
I(0) uncertainty (real space) i0_real_error2.2210e+06
Rg (reciprocal space) rg_reciprocal40.64
I(0) (reciprocal space) i0_reciprocal128700000.0000
Solution quality estimate total_estimate0.7966
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary29.6
Skewness Skewness skewness0.341
Kurtosis Kurtosis kurtosis-0.836
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9485000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.648; Smooth: 0.217

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1qr1a1
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_idd1qr1a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1qr1b_
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_idd1qr1d1
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_idd1qr1d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamilyd.19.1 — MHC antigen-recognition domain
Family Family familyd.19.1.1 — MHC antigen-recognition domain
Domain ID domain_idd1qr1e_
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)

CATH v4.4 (6 domains)

Domain ID domain_id1qr1A01
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_id1qr1A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1qr1B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1qr1D01
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_id1qr1D02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1qr1E00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)