6v3j

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

Method: X-RAY DIFFRACTION Dmax: 108.0 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 25–299 Not recorded Beta-2-microglobulin × 1 (P61769) Peptide Leu-Ser-Ser-Pro-Val-Thr-Lys-Ser-Phe × 1 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;14% PEG 3350, 2% tacsimate, pH 5.0, 0.1 M tri-sodium citrate pH 5.6 Resolution 1.98 Å R-free 0.236

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 1–275; 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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 21–119 Not recorded HLA-B alpha chain (B*5703GB) × 1 (I3ZN84) Peptide Leu-Ser-Ser-Pro-Val-Thr-Lys-Ser-Phe × 1 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;14% PEG 3350, 2% tacsimate, pH 5.0, 0.1 M tri-sodium citrate pH 5.6 Resolution 1.98 Å R-free 0.236

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

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 Not recorded HLA-B alpha chain (B*5703GB) × 1 (I3ZN84) Beta-2-microglobulin × 1 (P61769) Peptide Leu-Ser-Ser-Pro-Val-Thr-Lys-Ser-Phe × 1 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;14% PEG 3350, 2% tacsimate, pH 5.0, 0.1 M tri-sodium citrate pH 5.6 Resolution 1.98 Å R-free 0.236

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 1–299; 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 6v3j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6v3j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6v3j
Deposition date deposition_date2019-11-25
Structure title titleKIR3DL1 in complex with HLA-B*57:03 presenting the peptide LSSPVTKSF
Keywords keywordsPeptide Antigen, HLA, MHC, Immunity, 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_guinier31.51
Radius of gyration Rg (electron density) rg_electron30.92
Forward intensity I(0) i0100130000.00
Molecular weight molecular_weight77043.0 kDa
Excluded volume excluded_volume95447 ų
Envelope volume envelope_volume124230 ų
Hydration-shell volume shell_volume34990 ų
Envelope diameter envelope_diameter114.3
Shell Rg shell_rg36.42
Envelope Rg envelope_rg31.05
Shape Rg shape_rg30.91
Total Rg total_rg31.45
Total atoms total_atoms5436
Residues n_residues672
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 dmax108.0
Rg (real space) rg_real31.60
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real1.0010e+08
I(0) uncertainty (real space) i0_real_error1.6660e+06
Rg (reciprocal space) rg_reciprocal31.56
I(0) (reciprocal space) i0_reciprocal100100000.0000
Solution quality estimate total_estimate0.8767
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.7
Skewness Skewness skewness0.430
Kurtosis Kurtosis kurtosis-0.190
Angular range angular_range— – 0.2500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10360000.0000
Real-space data points n_real_points51
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.909

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id6v3jA01
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_id6v3jA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6v3jB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6v3jG01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6v3jG02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id6v3jG03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)