+Open data
-Basic information
Entry | Database: PDB / ID: 8eab | ||||||
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Title | NKG2D complexed with inhibitor 4f | ||||||
Components | NKG2-D type II integral membrane protein | ||||||
Keywords | IMMUNOSUPPRESSANT/INHIBITOR / NKG2D / Immune System / IMMUNOSUPPRESSANT / IMMUNOSUPPRESSANT-INHIBITOR complex | ||||||
Function / homology | Function and homology information negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / T cell costimulation / nitric oxide biosynthetic process ...negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / MHC class I protein binding / stimulatory C-type lectin receptor signaling pathway / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / DAP12 signaling / signaling receptor activity / carbohydrate binding / cellular response to lipopolysaccharide / adaptive immune response / cell differentiation / defense response to Gram-positive bacterium / external side of plasma membrane / cell surface / signal transduction / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å | ||||||
Authors | Thompson, A.A. / Grant, J.C. / Karpowich, N.K. / Sharma, S. | ||||||
Funding support | 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: Identification of small-molecule protein-protein interaction inhibitors for NKG2D. Authors: Thompson, A.A. / Harbut, M.B. / Kung, P.P. / Karpowich, N.K. / Branson, J.D. / Grant, J.C. / Hagan, D. / Pascual, H.A. / Bai, G. / Zavareh, R.B. / Coate, H.R. / Collins, B.C. / Cote, M. / ...Authors: Thompson, A.A. / Harbut, M.B. / Kung, P.P. / Karpowich, N.K. / Branson, J.D. / Grant, J.C. / Hagan, D. / Pascual, H.A. / Bai, G. / Zavareh, R.B. / Coate, H.R. / Collins, B.C. / Cote, M. / Gelin, C.F. / Damm-Ganamet, K.L. / Gholami, H. / Huff, A.R. / Limon, L. / Lumb, K.J. / Mak, P.A. / Nakafuku, K.M. / Price, E.V. / Shih, A.Y. / Tootoonchi, M. / Vellore, N.A. / Wang, J. / Wei, N. / Ziff, J. / Berger, S.B. / Edwards, J.P. / Gardet, A. / Sun, S. / Towne, J.E. / Venable, J.D. / Shi, Z. / Venkatesan, H. / Rives, M.L. / Sharma, S. / Shireman, B.T. / Allen, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eab.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eab.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 8eab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eab_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8eab_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8eab_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 8eab_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/8eab ftp://data.pdbj.org/pub/pdb/validation_reports/ea/8eab | HTTPS FTP |
-Related structure data
Related structure data | 8ea5C 8ea6C 8ea7C 8ea8C 8ea9C 8eaaC 1mpuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14880.832 Da / Num. of mol.: 2 / Mutation: S117E,I173S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLRK1, D12S2489E, NKG2D / Production host: Escherichia coli (E. coli) / References: UniProt: P26718 #2: Chemical | #3: Chemical | ChemComp-VN2 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 - 0.22 M NaNO3 20 - 31 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 30, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.44→35.53 Å / Num. obs: 50572 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.214 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.063 / Net I/σ(I): 8.5 / Num. measured all: 170411 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MPU Resolution: 1.44→34.03 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.67 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.44→34.03 Å
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Refine LS restraints |
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LS refinement shell |
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