7k81

KIR3DL1*005 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide

Method: X-RAY DIFFRACTION Dmax: 103.1 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt A0A411J078

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 25–300 Not recorded Beta-2-microglobulin × 1 (P61769) ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP × 1 KIR3DL1 × 1 (I6LEL9) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;298 K;14% PEG 3350, 2% tacsimate, pH 5.0, and 0.1 M trisodium citrate, pH 5.6 Resolution 2.00 Å R-free 0.243

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.

24 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A411J078_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–276; UniProt 25–300

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded MHC class I antigen × 1 (A0A411J078) ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP × 1 KIR3DL1 × 1 (I6LEL9) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;298 K;14% PEG 3350, 2% tacsimate, pH 5.0, and 0.1 M trisodium citrate, pH 5.6 Resolution 2.00 Å R-free 0.243

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

KIR3DL1

Homo sapiens

UniProt I6LEL9

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 27–315 Not recorded MHC class I antigen × 1 (A0A411J078) Beta-2-microglobulin × 1 (P61769) ARG-TYR-PRO-LEU-THR-PHE-GLY-TRP × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;298 K;14% PEG 3350, 2% tacsimate, pH 5.0, and 0.1 M trisodium citrate, pH 5.6 Resolution 2.00 Å R-free 0.243

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name I6LEL9_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain G; PDBConstruct 1–289; UniProt 27–315

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 7k81

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7k81
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7k81
Deposition date deposition_date2020-09-24
Structure title titleKIR3DL1*005 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide
Keywords keywordsKIR receptor, HLA, peptide presentation, 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_guinier31.05
Radius of gyration Rg (electron density) rg_electron30.47
Forward intensity I(0) i099012500.00
Molecular weight molecular_weight76243.0 kDa
Excluded volume excluded_volume94338 ų
Envelope volume envelope_volume123180 ų
Hydration-shell volume shell_volume34961 ų
Envelope diameter envelope_diameter109.7
Shell Rg shell_rg36.25
Envelope Rg envelope_rg30.57
Shape Rg shape_rg30.45
Total Rg total_rg31.04
Total atoms total_atoms5378
Residues n_residues664
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 dmax103.1
Rg (real space) rg_real31.11
Rg uncertainty (real space) rg_real_error0.83
I(0) (real space) i0_real9.9010e+07
I(0) uncertainty (real space) i0_real_error1.5960e+06
Rg (reciprocal space) rg_reciprocal31.09
I(0) (reciprocal space) i0_reciprocal99010000.0000
Solution quality estimate total_estimate0.8850
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4
Skewness Skewness skewness0.397
Kurtosis Kurtosis kurtosis-0.233
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10050000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.890

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id7k81G01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k81G02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id7k81G03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)