PDB-8pyw: Crystal structure of the human Nucleoside-diphosphate kinase B do...

ID or keywords:

Entry

Database: PDB / ID: 8pyw

Title

Crystal structure of the human Nucleoside-diphosphate kinase B domain bound to compound diphosphate form of AT-9052-Sp.

Components

Nucleoside diphosphate kinase B

Keywords

TRANSFERASE

Function / homology

Function and homology information

regulation of epidermis development / nucleoside triphosphate biosynthetic process / protein histidine kinase activity / Ribavirin ADME / G-quadruplex DNA binding / nucleoside-diphosphate kinase / positive regulation of keratinocyte differentiation / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / UTP biosynthetic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.553 Å

Authors

Feracci, M. / Chazot, A.

Funding support

France, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2024
Title: An exonuclease-resistant chain-terminating nucleotide analogue targeting the SARS-CoV-2 replicase complex.
Authors: Shannon, A. / Chazot, A. / Feracci, M. / Falcou, C. / Fattorini, V. / Selisko, B. / Good, S. / Moussa, A. / Sommadossi, J.P. / Ferron, F. / Alvarez, K. / Canard, B.

History

Deposition	Jul 26, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 27, 2023	Provider: repository / Type: Initial release
Revision 1.1	Feb 21, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pyw.cif.gz	963 KB	Display	PDBx/mmCIF format
PDB format	pdb8pyw.ent.gz	607.1 KB	Display	PDB format
PDBx/mmJSON format	8pyw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8pyw_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	8pyw_full_validation.pdf.gz	2.3 MB	Display
Data in XML	8pyw_validation.xml.gz	44.4 KB	Display
Data in CIF	8pyw_validation.cif.gz	63.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/py/8pyw ftp://data.pdbj.org/pub/pdb/validation_reports/py/8pyw	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.51093/xrd-00151 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #183 - Mar 2015 Phototropin similarity (1)

Deposited unit

A: Nucleoside diphosphate kinase B

B: Nucleoside diphosphate kinase B

C: Nucleoside diphosphate kinase B

D: Nucleoside diphosphate kinase B

E: Nucleoside diphosphate kinase B

F: Nucleoside diphosphate kinase B

hetero molecules

107 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	54.220, 121.060, 70.760
Angle α, β, γ (deg.)	90.000, 107.135, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 5 - 156 / Label seq-ID: 1 - 152

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30

#1: Protein	Nucleoside diphosphate kinase B / NDK B / NDP kinase B / C-myc purine-binding transcription factor PUF / Histidine protein kinase NDKB / nm23-H2 Mass: 17249.912 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NME2, NM23B / Production host: Escherichia coli (E. coli) References: UniProt: P22392, nucleoside-diphosphate kinase, histidine kinase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-IF9 / [[(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] dihydrogen phosphate Mass: 475.284 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C₁₁H₁₆FN₅O₉P₂S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 847 / 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: 2.14 Å³/Da / Density % sol: 42.64 % / Description: fragile thin needles
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: co-crystallisation with diphosphate AT-9052F compound.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980105 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980105 Å / Relative weight: 1
Reflection	Resolution: 1.553→48.668 Å / Num. obs: 121746 / % possible obs: 97.2 % / Redundancy: 3.9 % / CC_1/2: 0.997 / R_pim(I) all: 0.037 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.553→1.58 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5881 / CC_1/2: 0.723 / R_pim(I) all: 0.321 / % possible all: 93.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS	Jan 10, 2022 ; BUILT=20220110	data reduction
XSCALE	Jan 10, 2022 ; BUILT=20220820	data scaling
PHASER	VERSION 2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.553→48.668 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.957 / WR_factor R_free: 0.205 / WR_factor R_work: 0.173 / SU B: 3.527 / SU ML: 0.063 / Average fsc free: 0.9688 / Average fsc work: 0.9777 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.085
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1995	6018	4.943 %
R_work	0.1701	115727	-
all	0.172	-	-
obs	-	121745	97.161 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 20.57 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.709 Å²	-0 Å²	-0.046 Å²
2-	-	-0.395 Å²	-0 Å²
3-	-	-	0.952 Å²

Refinement step

Cycle: LAST / Resolution: 1.553→48.668 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7284	0	192	847	8323

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	7685
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7323
X-RAY DIFFRACTION	r_angle_refined_deg	1.738	1.668	10410
X-RAY DIFFRACTION	r_angle_other_deg	0.59	1.587	16893
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.484	5	920
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.35	5	54
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.806	20	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.484	10	1357
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.985	10	342
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	1112
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	8935
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1766
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	1415
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.179	0.2	6581
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	3715
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.075	0.2	3960
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.157	0.2	547
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.15	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.126	0.2	25
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.16	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	2.639	1.265	3656
X-RAY DIFFRACTION	r_mcbond_other	2.638	1.265	3656
X-RAY DIFFRACTION	r_mcangle_it	3.252	2.27	4563
X-RAY DIFFRACTION	r_mcangle_other	3.253	2.27	4564
X-RAY DIFFRACTION	r_scbond_it	6.639	1.736	4029
X-RAY DIFFRACTION	r_scbond_other	6.639	1.736	4029
X-RAY DIFFRACTION	r_scangle_it	8.09	3.013	5840
X-RAY DIFFRACTION	r_scangle_other	8.09	3.013	5841
X-RAY DIFFRACTION	r_lrange_it	7.646	14.118	8750
X-RAY DIFFRACTION	r_lrange_other	7.636	13.661	8556
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.075	0.05	4944
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.083	0.05	4940
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.077	0.05	4950
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.072	0.05	4970
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.078	0.05	4961
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.064	0.05	4925
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.058	0.05	4933
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.06	0.05	4930
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.06	0.05	4934
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.056	0.05	4954
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.061	0.05	4934
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.061	0.05	4946
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.05	0.05	4955
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.056	0.05	4951
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.064	0.05	4934

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07524	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07524	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08293	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08293	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07718	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07718	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07239	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07239	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07773	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07773	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06439	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06439	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.05832	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.05832	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.06031	0.05009
8	16	A	X-RAY DIFFRACTION	Local ncs	0.06031	0.05009
9	17	A	X-RAY DIFFRACTION	Local ncs	0.06001	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.06001	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.05591	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.05591	0.05009
11	21	A	X-RAY DIFFRACTION	Local ncs	0.0608	0.05009
11	22	A	X-RAY DIFFRACTION	Local ncs	0.0608	0.05009
12	23	A	X-RAY DIFFRACTION	Local ncs	0.06074	0.05009
12	24	A	X-RAY DIFFRACTION	Local ncs	0.06074	0.05009
13	25	A	X-RAY DIFFRACTION	Local ncs	0.0502	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.0502	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.05581	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.05581	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.064	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.064	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.553-1.593	0.264	424	0.237	8282	0.239	9259	0.951	0.958	94.0274	0.226
1.593-1.637	0.226	410	0.213	8180	0.213	9020	0.963	0.967	95.2328	0.198
1.637-1.684	0.242	416	0.205	8192	0.207	8719	0.953	0.971	98.7269	0.187
1.684-1.736	0.228	432	0.191	8042	0.193	8487	0.965	0.975	99.8468	0.172
1.736-1.793	0.205	368	0.17	7864	0.172	8248	0.974	0.98	99.806	0.151
1.793-1.856	0.213	409	0.173	7548	0.175	7987	0.97	0.981	99.6244	0.155
1.856-1.926	0.273	389	0.205	7197	0.209	7709	0.949	0.969	98.4045	0.182
1.926-2.004	0.208	375	0.181	6928	0.183	7419	0.969	0.979	98.4364	0.165
2.004-2.093	0.187	387	0.161	6646	0.162	7152	0.979	0.984	98.3361	0.153
2.093-2.195	0.195	306	0.157	6324	0.159	6750	0.974	0.985	98.2222	0.15
2.195-2.314	0.228	312	0.194	5789	0.195	6442	0.962	0.974	94.7066	0.18
2.314-2.454	0.188	298	0.15	5692	0.152	6178	0.978	0.986	96.9569	0.152
2.454-2.622	0.197	288	0.159	5325	0.161	5730	0.976	0.985	97.9581	0.163
2.622-2.832	0.181	251	0.155	4977	0.157	5394	0.977	0.985	96.9225	0.164
2.832-3.101	0.2	229	0.167	4508	0.169	4933	0.977	0.984	96.0268	0.179
3.101-3.465	0.192	194	0.171	4032	0.172	4463	0.98	0.985	94.6897	0.189
3.465-3.998	0.189	198	0.162	3516	0.164	3956	0.98	0.985	93.8827	0.185
3.998-4.888	0.146	151	0.133	2999	0.133	3355	0.989	0.991	93.8897	0.159
4.888-6.879	0.199	116	0.186	2365	0.187	2619	0.982	0.988	94.7308	0.219
6.879-48.668	0.188	65	0.175	1322	0.175	1479	0.989	0.988	93.7796	0.226

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	0.5228	-0.2357	-0.2015	1.7702	-0.2118	1.0908	-0.0023	-0.1026	0.0126	0.1123	-0.0215	-0.1784	-0.0705	0.157	0.0238	0.0123	-0.0107	-0.0145	0.0349	0.0057	0.0227	11.8091	23.5726	8.033
2	0.5889	-0.1725	0.1364	1.518	-0.0947	1.1679	-0.0015	-0.0923	-0.0996	0.0873	0.0048	0.2097	0.0405	-0.1764	-0.0033	0.008	-0.006	0.0138	0.0375	0.0112	0.0426	-12.6188	20.7328	7.2436
3	0.5027	0.0027	-0.0112	1.0162	0.3683	1.7408	-0.0339	0.052	0.0462	-0.0782	0.0124	-0.1181	-0.1027	0.198	0.0215	0.0149	-0.0161	-0.0002	0.0312	0.0139	0.0238	13.2819	37.1334	-22.7565
4	0.3587	0.3172	-0.1653	1.4739	-0.5198	1.5711	0.0284	0.0435	-0.114	-0.0928	-0.0456	-0.1986	0.1892	0.2431	0.0172	0.0419	0.0401	0.0047	0.0519	-0.0183	0.0647	12.4992	3.7116	-19.024
5	0.6515	0.4004	0.3258	1.4412	0.2229	1.9013	-0.0128	0.0041	0.1156	-0.0331	-0.0135	0.2206	-0.1248	-0.2307	0.0263	0.0132	0.0147	-0.0073	0.0317	0.0046	0.0439	-11.1993	39.5707	-20.6299
6	0.6482	-0.0376	-0.2442	0.9933	-0.0242	1.5566	0.0329	0.0907	-0.0504	-0.14	0.018	0.1846	0.1277	-0.2175	-0.0509	0.0427	-0.0198	-0.023	0.038	0.0002	0.0715	-11.7648	5.7509	-22.9491

Refinement TLS group

Selection: ALL

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Yorodumi