5e9d

RD-1 Mart-1 High bound to Mart-1 decameric peptide (ELA) in complex with HLA-A2

Method: X-RAY DIFFRACTION Dmax: 166.3 Å Quality: GOOD

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

HLA class I histocompatibility antigen, A-2 alpha 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) Melanoma derived Mart-1 peptide × 1 A6-TCR Valpha × 1 (A0A075B6T6) A6-TCR Vbeta × 1 (A0A0K0K1A5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;300 K;PEG 4000, 0.002 M Zinc Acetate, 5% 2- propanol. Resolution 2.51 Å R-free 0.232
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain F; UniProt 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) Melanoma derived Mart-1 peptide × 1 A6-TCR Valpha × 1 (A0A075B6T6) A6-TCR Vbeta × 1 (A0A0K0K1A5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;300 K;PEG 4000, 0.002 M Zinc Acetate, 5% 2- propanol. Resolution 2.51 Å R-free 0.232

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 F; 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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Melanoma derived Mart-1 peptide × 1 A6-TCR Valpha × 1 (A0A075B6T6) A6-TCR Vbeta × 1 (A0A0K0K1A5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;300 K;PEG 4000, 0.002 M Zinc Acetate, 5% 2- propanol. Resolution 2.51 Å R-free 0.232
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain G; UniProt 21–119 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Melanoma derived Mart-1 peptide × 1 A6-TCR Valpha × 1 (A0A075B6T6) A6-TCR Vbeta × 1 (A0A0K0K1A5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;300 K;PEG 4000, 0.002 M Zinc Acetate, 5% 2- propanol. Resolution 2.51 Å R-free 0.232

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 2–100; UniProt 21–119 Author chain G; PDBConstruct 2–100; UniProt 21–119

A6-TCR Valpha

Homo sapiens

UniProt A0A075B6T6

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain D; UniProt 22–112 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Melanoma derived Mart-1 peptide × 1 A6-TCR Vbeta × 1 (A0A0K0K1A5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;300 K;PEG 4000, 0.002 M Zinc Acetate, 5% 2- propanol. Resolution 2.51 Å R-free 0.232
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain I; UniProt 22–112 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Melanoma derived Mart-1 peptide × 1 A6-TCR Vbeta × 1 (A0A0K0K1A5) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;300 K;PEG 4000, 0.002 M Zinc Acetate, 5% 2- propanol. Resolution 2.51 Å R-free 0.232

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 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A075B6T6_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–91; UniProt 22–112 Author chain I; PDBConstruct 1–91; UniProt 22–112

A6-TCR Vbeta

Homo sapiens

UniProt A0A0K0K1A5

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 × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain E; UniProt 20–112 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Melanoma derived Mart-1 peptide × 1 A6-TCR Valpha × 1 (A0A075B6T6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;300 K;PEG 4000, 0.002 M Zinc Acetate, 5% 2- propanol. Resolution 2.51 Å R-free 0.232
2 Protein heterocomplex Heteromer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain J; UniProt 20–112 Not recorded HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) Melanoma derived Mart-1 peptide × 1 A6-TCR Valpha × 1 (A0A075B6T6) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;300 K;PEG 4000, 0.002 M Zinc Acetate, 5% 2- propanol. Resolution 2.51 Å R-free 0.232

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.

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A0K0K1A5_HUMAN
Isoform
PDB entities 5
Chains and sequence ranges Author chain E; PDBConstruct 20–112; UniProt 20–112 Author chain J; PDBConstruct 20–112; UniProt 20–112

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 5e9d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5e9d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5e9d
Deposition date deposition_date2015-10-15
Structure title titleRD-1 Mart-1 High bound to Mart-1 decameric peptide (ELA) in complex with HLA-A2
Keywords keywordssingle chain TCR-pMHC Complex, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier44.18
Radius of gyration Rg (electron density) rg_electron44.60
Forward intensity I(0) i0294873000.00
Molecular weight molecular_weight136230.0 kDa
Excluded volume excluded_volume168610 ų
Envelope volume envelope_volume239340 ų
Hydration-shell volume shell_volume48855 ų
Envelope diameter envelope_diameter173.6
Shell Rg shell_rg43.98
Envelope Rg envelope_rg44.80
Shape Rg shape_rg44.60
Total Rg total_rg44.58
Total atoms total_atoms9610
Residues n_residues1201
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 dmax166.3
Rg (real space) rg_real44.76
Rg uncertainty (real space) rg_real_error2.39
I(0) (real space) i0_real2.9490e+08
I(0) uncertainty (real space) i0_real_error5.8810e+06
Rg (reciprocal space) rg_reciprocal44.18
I(0) (reciprocal space) i0_reciprocal294700000.0000
Solution quality estimate total_estimate0.7772
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.0
Skewness Skewness skewness0.664
Kurtosis Kurtosis kurtosis0.092
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33830000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.572; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.548; Smooth: 0.833

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id5e9dA01
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_id5e9dA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e9dB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e9dD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e9dE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e9dF01
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_id5e9dF02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e9dG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e9dI00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5e9dJ00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)