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- PDB-3q2c: Binding properties to HLA class I molecules and the structure of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q2c | ||||||
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Title | Binding properties to HLA class I molecules and the structure of the leukocyte Ig-like receptor A3 (LILRA3/ILT6/LIR4/CD85e) | ||||||
![]() | Leukocyte immunoglobulin-like receptor subfamily A member 3 | ||||||
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Function / homology | ![]() neutrophil degranulation / tertiary granule membrane / ficolin-1-rich granule membrane / specific granule membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ryu, M. / Chen, Y. / Qi, J.X. / Liu, J. / Shi, Y. / Cheng, H. / Gao, G.F. | ||||||
![]() | ![]() Title: LILRA3 binds both classical and non-classical HLA class I molecules but with reduced affinities compared to LILRB1/LILRB2: structural evidence Authors: Ryu, M. / Chen, Y. / Qi, J. / Liu, J. / Fan, Z. / Nam, G. / Shi, Y. / Cheng, H. / Gao, G.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.6 KB | Display | ![]() |
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PDB format | ![]() | 36.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1vdgS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 10792.341 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, UNP residues 24-120 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Water | ChemComp-HOH / ![]() |
Sequence details | THE SEQUENCE IS BASED ON REFERENCE 3 OF DATABASE Q8N6C8 (LIRA3_HUMAN). RESIDUE VAL 82 (UNP RESIDUE ...THE SEQUENCE IS BASED ON REFERENCE 3 OF DATABASE Q8N6C8 (LIRA3_HUMAN). RESIDUE VAL 82 (UNP RESIDUE NUMBER 105) IS A SEQUENCE CONFLICT. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0M ammonium sulfate, 0.1M HEPES buffer (pH 7.5), 0.75% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 20, 2009 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→50 Å / Num. obs: 3558 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.5→2.59 Å / % possible all: 92.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1VDG Resolution: 2.5→23.947 Å / SU ML: 0.18 / σ(F): 0.16 / Phase error: 29.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.554 Å2 / ksol: 0.362 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→23.947 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 22.2116 Å / Origin y: 1.8417 Å / Origin z: 14.1459 Å
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Refinement TLS group | Selection details: all |