PDB-8ea7: NKG2D complexed with inhibitor 3g

ID or keywords:

Entry

Database: PDB / ID: 8ea7

Title

NKG2D complexed with inhibitor 3g

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 / 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.28 Å

Authors

Thompson, A.A. / Grant, J.C. / Karpowich, N.K. / Sharma, S.

Funding support

1items

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. / ...

History

Deposition	Aug 28, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 10, 2023	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8ea7.cif.gz	115.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ea7.ent.gz	91.9 KB	Display	PDB format
PDBx/mmJSON format	8ea7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ea/8ea7 ftp://data.pdbj.org/pub/pdb/validation_reports/ea/8ea7	HTTPS FTP

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Related structure data

Related structure data	8ea5C 8ea6C 8ea8C 8ea9C 8eaaC 8eabC 1mpuS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#232 - Apr 2019 Proteins and Biominerals similarity (6) #134 - Feb 2011 Integrin similarity (6) #75 - Mar 2006 Tissue Factor similarity (6) #261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #69 - Sep 2005 Cholera Toxin similarity (1)

Deposited unit

A: NKG2-D type II integral membrane protein

B: NKG2-D type II integral membrane protein

hetero molecules

30.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	100.582, 43.138, 67.545
Angle α, β, γ (deg.)	90.00, 107.42, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-463- HOH
2	1	A-481- HOH

#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 / 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	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-VMH / (4M)-N-{(1S)-2-(dimethylamino)-2-oxo-1-[3-(trifluoromethyl)phenyl]ethyl}-4-(1-methyl-1H-pyrazol-5-yl)-4'-(trifluoromethyl)[1,1'-biphenyl]-2-carboxamide Mass: 574.517 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₉H₂₄F₆N₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.64 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 16, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.28→39.35 Å / Num. obs: 61420 / % possible obs: 85.9 % / Redundancy: 3 % / CC_1/2: 0.998 / R_merge(I) obs: 0.043 / R_pim(I) all: 0.027 / R_rim(I) all: 0.051 / Net I/σ(I): 11.5 / Num. measured all: 187069
Reflection shell	Resolution: 1.28→1.3 Å / % possible obs: 30 % / Redundancy: 1.7 % / R_merge(I) obs: 0.664 / Num. measured all: 1811 / Num. unique obs: 1064 / CC_1/2: 0.571 / R_pim(I) all: 0.618 / R_rim(I) all: 0.91 / Net I/σ(I) obs: 1

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Phasing

Phasing	Method: molecular replacement
Phasing MR	Packing: 0

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
xia2		data scaling
PHASER		phasing
PDB_EXTRACT	3.27	data extraction
DIALS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1MPU

1mpu

Resolution: 1.28→39.35 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.95 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2147	2993	4.87 %
R_work	0.193	-	-
obs	0.1941	61397	85.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.28→39.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1920	0	55	145	2120

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2071
X-RAY DIFFRACTION	f_angle_d	0.851	2810
X-RAY DIFFRACTION	f_dihedral_angle_d	7.072	274
X-RAY DIFFRACTION	f_chiral_restr	0.086	274
X-RAY DIFFRACTION	f_plane_restr	0.005	366

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.28-1.3	0.2904	48	0.3323	956	X-RAY DIFFRACTION	30
1.3-1.32	0.345	67	0.3207	1228	X-RAY DIFFRACTION	39
1.32-1.35	0.2991	74	0.3101	1510	X-RAY DIFFRACTION	47
1.35-1.37	0.2566	99	0.2794	1841	X-RAY DIFFRACTION	57
1.37-1.4	0.3278	116	0.2681	2206	X-RAY DIFFRACTION	69
1.4-1.43	0.2728	127	0.2513	2523	X-RAY DIFFRACTION	78
1.43-1.46	0.2827	139	0.2582	2815	X-RAY DIFFRACTION	88
1.46-1.5	0.2516	162	0.2325	3124	X-RAY DIFFRACTION	97
1.5-1.54	0.2273	161	0.2227	3221	X-RAY DIFFRACTION	99
1.54-1.59	0.2519	151	0.2117	3199	X-RAY DIFFRACTION	100
1.59-1.64	0.2277	169	0.2045	3245	X-RAY DIFFRACTION	100
1.64-1.7	0.2013	184	0.2013	3198	X-RAY DIFFRACTION	100
1.7-1.76	0.2224	168	0.2077	3225	X-RAY DIFFRACTION	100
1.76-1.84	0.2411	159	0.2	3220	X-RAY DIFFRACTION	100
1.84-1.94	0.2161	132	0.1989	3290	X-RAY DIFFRACTION	100
1.94-2.06	0.2109	156	0.1949	3255	X-RAY DIFFRACTION	100
2.06-2.22	0.219	145	0.1914	3244	X-RAY DIFFRACTION	100
2.22-2.45	0.2104	185	0.1928	3247	X-RAY DIFFRACTION	100
2.45-2.8	0.2329	186	0.1949	3242	X-RAY DIFFRACTION	100
2.8-3.53	0.2302	175	0.1922	3272	X-RAY DIFFRACTION	100
3.53-39.35	0.1764	190	0.1669	3343	X-RAY DIFFRACTION	100

Refinement TLS params.

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

ID	L11 (°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)
1	5.695	3.1107	-0.6452	2.6654	-1.0137	0.6973	-0.3332	0.0586	0.6526	-0.4865	-0.0549	0.2049	-0.5134	0.2654	0.0983	0.3868	0.0238	-0.0663	0.2183	-0.0048	0.2686	-0.4996	-7.4454	8.2281
2	5.4358	2.1535	-2.7052	4.1985	-2.0897	7.4936	-0.0989	-0.0796	0.1125	-0.0231	0.0064	0.1707	-0.3115	-0.1569	0.0991	0.2078	0.0277	-0.0158	0.1426	-0.014	0.1293	-0.4394	-14.9524	12.0631
3	6.9254	0.522	-0.1875	6.8877	-2.7727	6.656	-0.0451	-0.3246	0.1168	0.398	-0.0434	0.4913	-0.3913	-0.6535	0.084	0.1452	0.0304	0.0348	0.2613	-0.035	0.1958	-12.5148	-21.7531	21.0951
4	6.5451	2.0274	-1.8945	4.5183	-0.125	6.3001	-0.2828	0.503	-0.3126	-0.4531	0.1345	-0.2104	0.0191	-0.1496	0.1006	0.2128	-0.0092	-0.0027	0.138	-0.0245	0.1089	-1.9504	-22.7291	7.942
5	8.1412	3.3442	-3.2396	6.3132	-2.3613	5.4336	0.1224	-0.3354	-0.2484	-0.2008	-0.1389	-0.4443	0.123	0.5203	0.0268	0.1315	0.0041	-0.0035	0.143	-0.0156	0.1656	5.2352	-23.6228	17.5479
6	4.0034	1.8304	0.091	5.538	3.062	4.3279	-0.3393	0.4059	-0.4148	-0.8521	-0.0019	0.6833	0.1076	-0.4952	0.167	0.287	-0.0599	-0.067	0.2494	-0.0533	0.2963	-8.9821	-31.4727	11.0729
7	6.3337	0.5871	0.8197	5.3998	-1.9379	6.449	0.1281	0.7583	-0.5384	-1.0204	0.0181	-0.4186	0.2021	0.5242	0.0301	0.3674	0.0193	0.0474	0.1763	-0.074	0.246	1.0669	-34.7541	8.9554
8	0.6713	0.2078	-1.6527	1.6628	-0.3338	4.0273	-0.1034	-0.9337	-0.5228	0.3618	0.2943	0.3082	0.7002	-0.2034	-0.1273	0.3436	-0.0288	-0.0764	0.2814	0.0537	0.3619	-5.7817	-39.5359	22.3789
9	3.2967	-0.745	-1.3957	5.7298	0.5283	4.9793	-0.0315	-0.2513	-0.2874	0.0337	0.0134	-0.0098	0.2001	-0.0978	0.0562	0.1306	-0.0235	-0.0098	0.1354	0.014	0.1777	-2.8966	-30.9869	20.4632
10	4.444	0.4262	-0.6063	5.1979	-3.378	2.2267	0.1737	0.6188	0.1422	-0.6877	-0.0105	-0.016	-0.0839	0.0013	-0.19	0.2728	0.0475	-0.0018	0.231	0.0013	0.1487	-6.0009	-17.796	10.7619
11	5.0539	1.6052	4.2259	1.001	1.2418	3.6873	-0.1064	0.6918	-0.2449	-0.2437	0.2202	-0.1563	-0.2109	0.5479	-0.1168	0.2222	-0.0509	0.0554	0.2691	-0.0403	0.1538	15.1346	-9.3267	13.2309
12	5.6993	-0.7692	0.953	2.531	0.4579	3.5682	-0.3768	-0.0555	0.4693	0.0529	0.1292	-0.1516	-0.6222	0.0577	0.145	0.2311	-0.0238	-0.0326	0.1006	-0.0263	0.1409	14.0825	-3.3629	24.3893
13	5.6478	-0.3625	0.6357	1.9271	0.9793	3.5039	-0.1788	-0.3006	-0.3306	0.0429	0.1445	-0.1773	-0.2157	0.2453	0.017	0.1476	-0.0144	0.0094	0.1385	0.0117	0.1847	18.7191	-8.7975	27.5936

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 93 through 103 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 104 through 114 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 115 through 130 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 131 through 143 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 144 through 153 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 154 through 173 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 174 through 182 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 183 through 188 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 189 through 208 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 209 through 216 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 94 through 130 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 131 through 179 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 180 through 214 )

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