9bl2

KIR3DL1*001 in complex with HLA-B*57:03 presenting the AW10 peptide

Method: X-RAY DIFFRACTION Dmax: 103.0 Å Quality: GOOD

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

HLA-B alpha chain (B*5703GB)

Homo sapiens

UniProt I3ZN84

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) Catenin alpha-1 peptide × 1 (P35221) Killer cell immunoglobulin-like receptor 3DL1 × 1 (P43629) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;294 K;18% PEG-3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6 Resolution 2.10 Å R-free 0.231

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.

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name I3ZN84_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 Fragment:UNP residues 21-119 HLA-B alpha chain (B*5703GB) × 1 (I3ZN84) Catenin alpha-1 peptide × 1 (P35221) Killer cell immunoglobulin-like receptor 3DL1 × 1 (P43629) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;294 K;18% PEG-3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6 Resolution 2.10 Å R-free 0.231

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

Catenin alpha-1 peptide

OrganismNot specified

UniProt P35221

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 C; UniProt 850–859 Fragment:residues 850-859 (Uniprot numbering) HLA-B alpha chain (B*5703GB) × 1 (I3ZN84) Beta-2-microglobulin × 1 (P61769) Killer cell immunoglobulin-like receptor 3DL1 × 1 (P43629) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;294 K;18% PEG-3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6 Resolution 2.10 Å R-free 0.231

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.

8 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CTNA1_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 850–859

Killer cell immunoglobulin-like receptor 3DL1

Homo sapiens

UniProt P43629

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 22–320 Fragment:residues 1-299 HLA-B alpha chain (B*5703GB) × 1 (I3ZN84) Beta-2-microglobulin × 1 (P61769) Catenin alpha-1 peptide × 1 (P35221) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.6;294 K;18% PEG-3350, 2% tacsimate pH 5.0, 0.1 M tri-sodium citrate pH 5.6 Resolution 2.10 Å R-free 0.231

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 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KI3L1_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain G; PDBConstruct 18–316; UniProt 22–320

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 9bl2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9bl2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9bl2
Deposition date deposition_date2024-04-29
Structure title titleKIR3DL1*001 in complex with HLA-B*57:03 presenting the AW10 peptide
Keywords keywordsimmunoglobulin fold, natural killer cell receptor, Kir, 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_guinier31.19
Radius of gyration Rg (electron density) rg_electron30.61
Forward intensity I(0) i097561400.00
Molecular weight molecular_weight75811.0 kDa
Excluded volume excluded_volume93850 ų
Envelope volume envelope_volume121720 ų
Hydration-shell volume shell_volume34603 ų
Envelope diameter envelope_diameter110.5
Shell Rg shell_rg36.08
Envelope Rg envelope_rg30.66
Shape Rg shape_rg30.61
Total Rg total_rg31.10
Total atoms total_atoms5353
Residues n_residues675
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 dmax103.0
Rg (real space) rg_real31.26
Rg uncertainty (real space) rg_real_error0.82
I(0) (real space) i0_real9.7560e+07
I(0) uncertainty (real space) i0_real_error1.4880e+06
Rg (reciprocal space) rg_reciprocal31.24
I(0) (reciprocal space) i0_reciprocal97560000.0000
Solution quality estimate total_estimate0.8842
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.4
Skewness Skewness skewness0.410
Kurtosis Kurtosis kurtosis-0.225
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9914000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.860

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

8. Citations (1)

9. Files and Curves (10)