9l4i

Crystal structure of HLA-C*14:02 complexed with KIR2DL2

Method: X-RAY DIFFRACTION Dmax: 108.8 Å Quality: GOOD

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

MHC class I antigen

Homo sapiens

UniProt G9MDC7

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 1–273 Not recorded Beta-2-microglobulin × 1 (P61769) LL8 × 1 Killer cell immunoglobulin-like receptor 2DL2 × 1 (P43627) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277.15 K;0.2 M Potassium citrate tribasic monohydrate and 20% w/v Polyethylene glycol 3,350 Resolution 2.50 Å R-free 0.253

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 G9MDC7_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–273; UniProt 1–273

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 (G9MDC7) LL8 × 1 Killer cell immunoglobulin-like receptor 2DL2 × 1 (P43627) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277.15 K;0.2 M Potassium citrate tribasic monohydrate and 20% w/v Polyethylene glycol 3,350 Resolution 2.50 Å R-free 0.253

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 2DL2

Homo sapiens

UniProt P43627

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 D; UniProt 26–221 Not recorded MHC class I antigen × 1 (G9MDC7) Beta-2-microglobulin × 1 (P61769) LL8 × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;277.15 K;0.2 M Potassium citrate tribasic monohydrate and 20% w/v Polyethylene glycol 3,350 Resolution 2.50 Å R-free 0.253

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.

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KI2L2_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–196; UniProt 26–221

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 9l4i

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9l4i
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9l4i
Deposition date deposition_date2024-12-20
Structure title titleCrystal structure of HLA-C*14:02 complexed with KIR2DL2
Keywords keywordsHLA-C; KIR2DL2, 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_guinier31.30
Radius of gyration Rg (electron density) rg_electron31.25
Forward intensity I(0) i070163300.00
Molecular weight molecular_weight63946.0 kDa
Excluded volume excluded_volume79059 ų
Envelope volume envelope_volume106460 ų
Hydration-shell volume shell_volume31017 ų
Envelope diameter envelope_diameter115.3
Shell Rg shell_rg35.16
Envelope Rg envelope_rg31.49
Shape Rg shape_rg31.23
Total Rg total_rg31.64
Total atoms total_atoms4516
Residues n_residues558
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 dmax108.8
Rg (real space) rg_real31.60
Rg uncertainty (real space) rg_real_error1.07
I(0) (real space) i0_real7.0160e+07
I(0) uncertainty (real space) i0_real_error1.1090e+06
Rg (reciprocal space) rg_reciprocal31.48
I(0) (reciprocal space) i0_reciprocal70160000.0000
Solution quality estimate total_estimate0.8384
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.1
Skewness Skewness skewness0.592
Kurtosis Kurtosis kurtosis-0.043
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7768000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.768; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.777; Smooth: 0.813

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)