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- PDB-8se6: NKG2D complexed with inhibitor 36 -

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Basic information

Entry
Database: PDB / ID: 8se6
TitleNKG2D complexed with inhibitor 36
ComponentsNKG2-D type II integral membrane protein
KeywordsIMMUNE SYSTEM/INHIBITOR / NKG2D / DEL / cryptic pocket / immunoreceptors / Immune System / SIGNALING PROTEIN / IMMUNE SYSTEM-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / positive regulation of natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / T cell costimulation / nitric oxide biosynthetic process ...negative regulation of natural killer cell chemotaxis / MHC class Ib receptor activity / natural killer cell mediated cytotoxicity / natural killer cell activation / negative regulation of GTPase activity / positive regulation of natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / MHC class I protein binding / T cell costimulation / nitric oxide biosynthetic process / DAP12 interactions / positive regulation of nitric oxide biosynthetic process / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / membrane / identical protein binding / plasma membrane
Similarity search - Function
NKG2-D type II integral membrane protein / Natural killer cell receptor-like, C-type lectin-like domain / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Chem-ZWA / NKG2-D type II integral membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsThompson, A.A. / Grant, J.C. / Karpowich, N.K. / Sharma, S.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2023
Title: Development of small molecule inhibitors of natural killer group 2D receptor (NKG2D).
Authors: Wang, J. / Nakafuku, K.M. / Ziff, J. / Gelin, C.F. / Gholami, H. / Thompson, A.A. / Karpowich, N.K. / Limon, L. / Coate, H.R. / Damm-Ganamet, K.L. / Shih, A.Y. / Grant, J.C. / Cote, M. / ...Authors: Wang, J. / Nakafuku, K.M. / Ziff, J. / Gelin, C.F. / Gholami, H. / Thompson, A.A. / Karpowich, N.K. / Limon, L. / Coate, H.R. / Damm-Ganamet, K.L. / Shih, A.Y. / Grant, J.C. / Cote, M. / Mak, P.A. / Pascual, H.A. / Rives, M.L. / Edwards, J.P. / Venable, J.D. / Venkatesan, H. / Shi, Z. / Allen, S.J. / Sharma, S. / Kung, P.P. / Shireman, B.T.
History
DepositionApr 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NKG2-D type II integral membrane protein
B: NKG2-D type II integral membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1208
Polymers29,7622
Non-polymers1,3586
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-5 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.041, 43.483, 64.188
Angle α, β, γ (deg.)90.00, 102.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-448-

HOH

21B-496-

HOH

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Components

#1: Protein NKG2-D type II integral membrane protein / Killer cell lectin-like receptor subfamily K member 1 / NK cell receptor D / NKG2-D-activating NK receptor


Mass: 14880.832 Da / Num. of mol.: 2
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
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-ZWA / N-[(1S)-2-(dimethylamino)-2-oxo-1-{3-[3-(2,2,2-trifluoroethyl)azetidin-1-yl]phenyl}ethyl]-4'-(trifluoromethyl)[1,1'-biphenyl]-2-carboxamide


Mass: 563.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H27F6N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.15 - 0.22 M NaNO3, 20- 31 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.36→62.58 Å / Num. obs: 52859 / % possible obs: 91.1 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.032 / Rrim(I) all: 0.059 / Net I/σ(I): 9.9 / Num. measured all: 172740
Reflection shellResolution: 1.36→1.38 Å / % possible obs: 49.1 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.778 / Num. measured all: 3361 / Num. unique obs: 1395 / CC1/2: 0.713 / Rpim(I) all: 0.573 / Rrim(I) all: 0.972 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→43.44 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2108 2617 4.96 %
Rwork0.194 --
obs0.1948 52815 91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 93 162 2213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062112
X-RAY DIFFRACTIONf_angle_d0.912848
X-RAY DIFFRACTIONf_dihedral_angle_d10.562294
X-RAY DIFFRACTIONf_chiral_restr0.089282
X-RAY DIFFRACTIONf_plane_restr0.005362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.4875860.38751395X-RAY DIFFRACTION49
1.38-1.410.3954900.35711653X-RAY DIFFRACTION58
1.41-1.440.3591050.33461965X-RAY DIFFRACTION67
1.44-1.470.36121360.3212350X-RAY DIFFRACTION82
1.47-1.510.29671650.29292643X-RAY DIFFRACTION93
1.51-1.540.27641520.26412777X-RAY DIFFRACTION96
1.54-1.580.26631700.242767X-RAY DIFFRACTION98
1.58-1.630.20421380.22632823X-RAY DIFFRACTION97
1.63-1.680.26021370.21262856X-RAY DIFFRACTION97
1.68-1.740.2191430.20172827X-RAY DIFFRACTION98
1.74-1.810.20521460.1942840X-RAY DIFFRACTION98
1.81-1.90.18381290.18622880X-RAY DIFFRACTION99
1.9-20.21641470.1832847X-RAY DIFFRACTION99
2-2.120.19331480.17712865X-RAY DIFFRACTION99
2.12-2.290.19941360.17882939X-RAY DIFFRACTION99
2.29-2.520.18611370.17492895X-RAY DIFFRACTION100
2.52-2.880.18221400.18292935X-RAY DIFFRACTION100
2.88-3.630.19021590.18462933X-RAY DIFFRACTION100
3.63-43.440.19251530.17323008X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8961.6313-0.73963.3381-1.12791.8367-0.00630.01440.0982-0.01220.01330.3192-0.1306-0.1302-0.00880.13880.00470.00110.1595-0.0060.1111-2.6819-15.607614.141
23.77140.319-0.38382.55390.08434.3914-0.00050.1315-0.3854-0.27810.03940.03380.24490.0091-0.03740.16820.0046-0.01320.1091-0.0270.17180.5479-26.479711.9975
33.9653-1.3383-0.5542.5417-1.78714.5598-0.00240.0552-0.2507-0.1284-0.03570.16370.3456-0.090.02890.2247-0.0246-0.06720.1268-0.05080.3083-1.2941-34.578711.5376
42.7130.7101-0.75573.64080.03131.0410.06820.0191-0.2796-0.1401-0.01950.10940.0552-0.0822-0.06640.1336-0.0134-0.01070.1614-0.01180.1702-1.5738-26.743916.8153
50.0546-0.0621-0.27080.71260.59683.9517-0.06820.3783-0.2455-0.1480.01390.2345-0.3320.09310.06770.2381-0.0097-0.01610.20770.00080.20075.59-6.69296.7488
64.3881-1.5172.93883.6281-0.77394.38230.01210.14720.0078-0.17610.00320.0213-0.1147-0.01920.0580.1947-0.03270.00460.15610.00530.11410.8966-8.484313.4605
74.52861.00182.20311.6101-0.37987.47780.0440.6825-0.515-0.23220.1657-0.2360.08570.4143-0.17750.1304-0.0160.06120.2752-0.06680.195226.707-11.022615.5829
83.2825-0.8220.89722.75410.08811.8856-0.0895-0.023-0.04040.01910.02550.1318-0.1079-0.06230.04830.1219-0.00290.02090.1093-0.00070.07814.6278-6.29422.1623
98.21611.5714.89482.94443.32155.0694-0.3717-0.46611.27090.73820.258-0.9435-0.73650.40680.1040.4367-0.0392-0.09840.275-0.06130.395924.47342.6726.989
102.41750.9052-0.73282.6302-1.81343.7616-0.22440.19420.5156-0.20540.03880.0424-0.31380.09690.17010.2896-0.0363-0.06540.15920.00850.284416.96453.121225.6819
112.9931-0.03790.69471.37360.66711.9243-0.06710.0033-0.05520.03430.0489-0.1317-0.04280.10690.01550.1083-0.01410.02540.11040.01150.111421.0695-8.649326.0354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 92 through 130 )
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 167 )
3X-RAY DIFFRACTION3chain 'A' and (resid 168 through 188 )
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 216 )
5X-RAY DIFFRACTION5chain 'B' and (resid 92 through 103 )
6X-RAY DIFFRACTION6chain 'B' and (resid 104 through 114 )
7X-RAY DIFFRACTION7chain 'B' and (resid 115 through 130 )
8X-RAY DIFFRACTION8chain 'B' and (resid 131 through 159 )
9X-RAY DIFFRACTION9chain 'B' and (resid 160 through 168 )
10X-RAY DIFFRACTION10chain 'B' and (resid 169 through 179 )
11X-RAY DIFFRACTION11chain 'B' and (resid 180 through 215 )

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