PDB-8pie: Crystal structure of the human nucleoside diphosphate kinase B do...

ID or keywords:

Entry

Database: PDB / ID: 8pie

Title

Crystal structure of the human nucleoside diphosphate kinase B domain in complex with the product AT-8500 formed by catalysis of compound AT-9010

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 / UTP biosynthetic process / CTP biosynthetic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Feracci, M. / Chazot, A. / Ferron, F. / Alvarez, K. / Canard, B.

Funding support

France, 1items

Citation

Journal: Plos Biol. / Year: 2024
Title: The activation cascade of the broad-spectrum antiviral bemnifosbuvir characterized at atomic resolution.
Authors: Chazot, A. / Zimberger, C. / Feracci, M. / Moussa, A. / Good, S. / Sommadossi, J.P. / Alvarez, K. / Ferron, F. / Canard, B.

History

Deposition	Jun 21, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 31, 2024	Provider: repository / Type: Initial release
Revision 1.1	Sep 4, 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.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8pie.cif.gz	380.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8pie.ent.gz	304.4 KB	Display	PDB format
PDBx/mmJSON format	8pie.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8pie_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	8pie_full_validation.pdf.gz	2.3 MB	Display
Data in XML	8pie_validation.xml.gz	40.9 KB	Display
Data in CIF	8pie_validation.cif.gz	55.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pi/8pie ftp://data.pdbj.org/pub/pdb/validation_reports/pi/8pie	HTTPS FTP

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Related structure data

Related structure data	8ptsC 8pwkC 8qchC C: citing same article (ref.)
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-00152 / 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

120 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)	54.190, 120.313, 71.918
Angle α, β, γ (deg.)	90.000, 110.154, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 6 - 156 / Label seq-ID: 21 - 171

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: 19547.240 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-7QT / [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate / AT-8500 Mass: 459.218 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₁H₁₆FN₅O₁₀P₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.12 Å³/Da / Density % sol: 41.89 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: mixing 1:1 ration with precipitant solution composed of: -50mM Tris-HCl pH8.4 -12% PEG3350 -16% glycerol

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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: 0.98010736891201 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98010736891201 Å / Relative weight: 1
Reflection	Resolution: 1.9→49.68 Å / Num. obs: 67263 / % possible obs: 98.89 % / Redundancy: 7.1 % / CC_1/2: 0.996 / R_pim(I) all: 0.0552 / Net I/σ(I): 8.61
Reflection shell	Resolution: 1.9→1.968 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.57 / Num. unique obs: 6623 / CC_1/2: 0.793 / R_pim(I) all: 0.3295 / % possible all: 98

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→49.68 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.941 / SU B: 3.633 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.165 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.213	3342	4.969 %
R_work	0.1724	63919	-
all	0.174	-	-
obs	-	67261	98.902 %

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: 24.719 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.471 Å²	-0 Å²	-0.662 Å²
2-	-	0.22 Å²	0 Å²
3-	-	-	0.58 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→49.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7284	0	180	402	7866

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.012	7647
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7269
X-RAY DIFFRACTION	r_angle_refined_deg	2.05	1.663	10368
X-RAY DIFFRACTION	r_angle_other_deg	0.699	1.577	16757
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.536	5	902
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.869	5	54
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.026	5	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.821	10	1351
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.857	10	342
X-RAY DIFFRACTION	r_chiral_restr	0.119	0.2	1106
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	8713
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1759
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	1408
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.192	0.2	6684
X-RAY DIFFRACTION	r_nbtor_refined	0.188	0.2	3795
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	3994
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.185	0.2	340
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.243	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.453	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.336	0.2	25
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.321	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	2.881	2.146	3620
X-RAY DIFFRACTION	r_mcbond_other	2.881	2.146	3620
X-RAY DIFFRACTION	r_mcangle_it	3.578	3.838	4515
X-RAY DIFFRACTION	r_mcangle_other	3.578	3.838	4516
X-RAY DIFFRACTION	r_scbond_it	5.694	2.901	4027
X-RAY DIFFRACTION	r_scbond_other	5.694	2.901	4027
X-RAY DIFFRACTION	r_scangle_it	8.248	5.111	5852
X-RAY DIFFRACTION	r_scangle_other	8.247	5.112	5853
X-RAY DIFFRACTION	r_lrange_it	8.374	23.306	8643
X-RAY DIFFRACTION	r_lrange_other	8.362	23.178	8573
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.063	0.05	4967
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.066	0.05	4942
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.067	0.05	4961
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.067	0.05	4965
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.07	0.05	4944
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.071	0.05	4949
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.067	0.05	4957
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.064	0.05	4969
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.069	0.05	4944
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.075	0.05	4968
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.058	0.05	4993
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.074	0.05	4976
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.073	0.05	4952
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.071	0.05	4952
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.055	0.05	4992

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	0.06258	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.06258	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.06569	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.06569	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06744	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06744	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06681	0.05009
4	8	A	X-RAY DIFFRACTION	Local ncs	0.06681	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07005	0.05009
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07005	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.07072	0.05009
6	12	A	X-RAY DIFFRACTION	Local ncs	0.07072	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.06731	0.05009
7	14	A	X-RAY DIFFRACTION	Local ncs	0.06731	0.05009
8	15	A	X-RAY DIFFRACTION	Local ncs	0.06362	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.06362	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.0689	0.05009
9	18	A	X-RAY DIFFRACTION	Local ncs	0.0689	0.05009
10	19	A	X-RAY DIFFRACTION	Local ncs	0.075	0.05009
10	20	A	X-RAY DIFFRACTION	Local ncs	0.075	0.05009
11	21	A	X-RAY DIFFRACTION	Local ncs	0.05761	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.05761	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.07425	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.07425	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.07313	0.05009
13	26	A	X-RAY DIFFRACTION	Local ncs	0.07313	0.05009
14	27	A	X-RAY DIFFRACTION	Local ncs	0.07072	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.07072	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.05498	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.05498	0.0501

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 (%)
1.9-1.949	0.272	242	0.224	4680	X-RAY DIFFRACTION	98.0088
1.949-2.003	0.257	256	0.22	4572	X-RAY DIFFRACTION	98.17
2.003-2.061	0.251	254	0.196	4388	X-RAY DIFFRACTION	98.3058
2.061-2.124	0.248	243	0.197	4272	X-RAY DIFFRACTION	98.2804
2.124-2.193	0.215	243	0.177	4154	X-RAY DIFFRACTION	98.5212
2.193-2.27	0.238	232	0.176	4052	X-RAY DIFFRACTION	98.6642
2.27-2.356	0.205	211	0.16	3914	X-RAY DIFFRACTION	98.7551
2.356-2.452	0.228	195	0.177	3787	X-RAY DIFFRACTION	98.7844
2.452-2.56	0.203	180	0.166	3641	X-RAY DIFFRACTION	99.0923
2.56-2.685	0.24	158	0.163	3468	X-RAY DIFFRACTION	99.0981
2.685-2.83	0.208	173	0.157	3337	X-RAY DIFFRACTION	99.2647
2.83-3.001	0.216	140	0.171	3177	X-RAY DIFFRACTION	99.3114
3.001-3.207	0.239	149	0.178	2942	X-RAY DIFFRACTION	99.5171
3.207-3.463	0.218	123	0.176	2756	X-RAY DIFFRACTION	99.5161
3.463-3.792	0.193	145	0.175	2536	X-RAY DIFFRACTION	99.6284
3.792-4.236	0.185	109	0.16	2324	X-RAY DIFFRACTION	99.754
4.236-4.886	0.166	88	0.148	2065	X-RAY DIFFRACTION	99.8146
4.886-5.969	0.162	78	0.161	1741	X-RAY DIFFRACTION	99.8902
5.969-8.382	0.202	76	0.162	1336	X-RAY DIFFRACTION	99.9292
8.382-49.68	0.216	47	0.173	777	X-RAY DIFFRACTION	100

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