6zkw

Crystal structure of InhA:01 TCR in complex with HLA-E bound to InhA (53-61)

Method: X-RAY DIFFRACTION Dmax: 130.6 Å Quality: GOOD

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

HLA class I histocompatibility antigen, alpha chain E

Homo sapiens

UniProt P13747

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 22–297 Not recorded Beta-2-microglobulin × 1 (P61769) Enoyl-[acyl-carrier-protein] reductase [NADH] × 1 (P9WGR1) T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293.15 K;0.1 M TRIS pH 8.5, 25 % (w/v) PEG 4000, 15 % Glycerol Resolution 2.26 Å R-free 0.287

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.

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

View Construct and Data Evidence
UniProt name HLAE_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 22–297

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, alpha chain E × 1 (P13747) Enoyl-[acyl-carrier-protein] reductase [NADH] × 1 (P9WGR1) T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293.15 K;0.1 M TRIS pH 8.5, 25 % (w/v) PEG 4000, 15 % Glycerol Resolution 2.26 Å R-free 0.287

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

Enoyl-[acyl-carrier-protein] reductase [NADH]

OrganismNot specified

UniProt P9WGR1

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 C; UniProt 53–61 Not recorded HLA class I histocompatibility antigen, alpha chain E × 1 (P13747) Beta-2-microglobulin × 1 (P61769) T-cell receptor alpha chain × 1 T-cell receptor beta chain × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293.15 K;0.1 M TRIS pH 8.5, 25 % (w/v) PEG 4000, 15 % Glycerol Resolution 2.26 Å R-free 0.287

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.

52 other PDB entries and 70 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INHA_MYCTU
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 53–61

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 6zkw

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6zkw
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6zkw
Deposition date deposition_date2020-06-30
Structure title titleCrystal structure of InhA:01 TCR in complex with HLA-E bound to InhA (53-61)
Keywords keywordsT cell receptor, TCR, HLA-E, InhA, 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_guinier37.40
Radius of gyration Rg (electron density) rg_electron37.77
Forward intensity I(0) i0139706000.00
Molecular weight molecular_weight91905.0 kDa
Excluded volume excluded_volume113510 ų
Envelope volume envelope_volume154820 ų
Hydration-shell volume shell_volume37455 ų
Envelope diameter envelope_diameter137.8
Shell Rg shell_rg39.31
Envelope Rg envelope_rg38.08
Shape Rg shape_rg37.77
Total Rg total_rg37.86
Total atoms total_atoms6480
Residues n_residues813
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 dmax130.6
Rg (real space) rg_real38.03
Rg uncertainty (real space) rg_real_error1.38
I(0) (real space) i0_real1.3970e+08
I(0) uncertainty (real space) i0_real_error2.4490e+06
Rg (reciprocal space) rg_reciprocal37.64
I(0) (reciprocal space) i0_reciprocal139700000.0000
Solution quality estimate total_estimate0.7786
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.2
Skewness Skewness skewness0.677
Kurtosis Kurtosis kurtosis-0.114
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16220000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.630; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.723; Smooth: 0.506

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6zkwA01
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_id6zkwA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)