PDB-8qw2: Human NDPK-C in complex with UDP and Mg2+

ID or keywords:

Entry

Database: PDB / ID: 8qw2

Title

Human NDPK-C in complex with UDP and Mg2+

Components

Nucleoside diphosphate kinase 3

Keywords

TRANSFERASE / Kinase

Function / homology

Function and homology information

nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / mitochondrial fusion / GTP biosynthetic process / nucleoside diphosphate kinase activity / ciliary basal body / mitochondrial outer membrane ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 1.87 Å

Authors

Werten, S. / Amjadi, R. / Scheffzek, K.

Funding support

1items

Citation

Journal: Int J Mol Sci / Year: 2024
Title: Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes.
Authors: Amjadi, R. / Werten, S. / Lomada, S.K. / Baldin, C. / Scheffzek, K. / Dunzendorfer-Matt, T. / Wieland, T.

History

Deposition	Oct 18, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 18, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2024	Group: Database references / Structure summary / Category: citation / pdbx_entry_details Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qw2.cif.gz	504.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8qw2.ent.gz	319.6 KB	Display	PDB format
PDBx/mmJSON format	8qw2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8qw2_validation.pdf.gz	5.2 MB	Display	wwPDB validaton report
Full document	8qw2_full_validation.pdf.gz	5.2 MB	Display
Data in XML	8qw2_validation.xml.gz	42.9 KB	Display
Data in CIF	8qw2_validation.cif.gz	55.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qw/8qw2 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/8qw2	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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Nucleoside diphosphate kinase 3

B: Nucleoside diphosphate kinase 3

C: Nucleoside diphosphate kinase 3

D: Nucleoside diphosphate kinase 3

E: Nucleoside diphosphate kinase 3

F: Nucleoside diphosphate kinase 3

hetero molecules

108 kDa, 6 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)	106.532, 115.991, 83.842
Angle α, β, γ (deg.)	90.000, 93.281, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	F-326- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 18 - 169 / Label seq-ID: 4 - 155

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 3 Mass: 17545.137 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NME3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13232
#2: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / Details: 27% glycerol, 7% PEG 8000, 40 mM KH2PO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.6888 Å
Detector	Type: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 9, 2021 / Details: Toroidal mirror
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.6888 Å / Relative weight: 1
Reflection	Resolution: 1.87→47.717 Å / Num. obs: 83689 / % possible obs: 99.9 % / Redundancy: 5.2 % / B_iso Wilson estimate: 44 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.042 / R_pim(I) all: 0.02 / R_rim(I) all: 0.047 / Net I/σ(I): 15
Reflection shell	Resolution: 1.87→1.94 Å / Redundancy: 4.9 % / R_merge(I) obs: 1.187 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8175 / CC_1/2: 0.697 / R_pim(I) all: 0.592 / R_rim(I) all: 1.331 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS / Resolution: 1.87→47.717 Å / Cor.coef. F_o:F_c: 0.98 / Cor.coef. F_o:F_c free: 0.969 / SU B: 10.752 / SU ML: 0.137 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2026	2091	2.501 %
R_work	0.1704	81503	-
all	0.171	-	-
obs	-	83594	99.722 %

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: 58.175 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	-0 Å²	2.016 Å²
2-	-	-0.875 Å²	-0 Å²
3-	-	-	0.6 Å²

Refinement step

Cycle: LAST / Resolution: 1.87→47.717 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7284	0	156	313	7753

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	7620
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7242
X-RAY DIFFRACTION	r_angle_refined_deg	1.618	1.664	10388
X-RAY DIFFRACTION	r_angle_other_deg	0.514	1.581	16572
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.499	5	910
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.638	5	98
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.211	10	1272
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.884	10	362
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1118
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	9204
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1908
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1435
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	6773
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	3738
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	4114
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.166	0.2	354
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.129	0.2	8
X-RAY DIFFRACTION	r_metal_ion_refined	0.087	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.16	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.184	0.2	62
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.176	0.2	15
X-RAY DIFFRACTION	r_mcbond_it	3.548	3.776	3646
X-RAY DIFFRACTION	r_mcbond_other	3.544	3.775	3646
X-RAY DIFFRACTION	r_mcangle_it	4.56	6.801	4566
X-RAY DIFFRACTION	r_mcangle_other	4.531	6.76	4549
X-RAY DIFFRACTION	r_scbond_it	5.251	4.467	3974
X-RAY DIFFRACTION	r_scbond_other	5.254	4.466	3967
X-RAY DIFFRACTION	r_scangle_it	7.505	7.992	5829
X-RAY DIFFRACTION	r_scangle_other	7.504	7.99	5826
X-RAY DIFFRACTION	r_lrange_it	9.083	38.436	8507
X-RAY DIFFRACTION	r_lrange_other	9.092	38.027	8466
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.075	0.05	4924
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.076	0.05	4914
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.072	0.05	4921
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.072	0.05	4869
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.079	0.05	4897
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.064	0.05	4939
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.081	0.05	4885
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.073	0.05	4906
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.064	0.05	4950
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.072	0.05	4856
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.075	0.05	4883
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.072	0.05	4904
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.075	0.05	4904
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.066	0.05	4925
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.056	0.05	4939

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	0.07502	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07502	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07641	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07641	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07153	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.07153	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.07166	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.07166	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07877	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07877	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06402	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.06402	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.08137	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.08137	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.07312	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.07312	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.06409	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.06409	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.07185	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.07185	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.07535	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.07535	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.07205	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.07205	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.0748	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.0748	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.06628	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.06628	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.05614	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.05614	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
1.87-1.919	0.491	159	0.473	5912	0.473	6183	0.772	0.8	98.1886	0.459
1.919-1.971	0.388	127	0.392	5855	0.392	6009	0.854	0.856	99.5507	0.37
1.971-2.028	0.329	157	0.336	5665	0.336	5829	0.895	0.896	99.8799	0.305
2.028-2.09	0.351	171	0.29	5507	0.291	5695	0.898	0.925	99.7015	0.247
2.09-2.159	0.278	141	0.253	5355	0.253	5497	0.946	0.949	99.9818	0.216
2.159-2.234	0.274	102	0.22	5237	0.221	5345	0.95	0.964	99.8877	0.187
2.234-2.319	0.229	108	0.193	5056	0.194	5165	0.972	0.976	99.9806	0.166
2.319-2.413	0.236	113	0.189	4812	0.191	4926	0.966	0.979	99.9797	0.165
2.413-2.52	0.212	122	0.188	4639	0.189	4763	0.971	0.98	99.958	0.168
2.52-2.643	0.226	146	0.183	4413	0.185	4559	0.97	0.981	100	0.166
2.643-2.785	0.211	107	0.174	4211	0.175	4319	0.972	0.983	99.9768	0.165
2.785-2.953	0.211	127	0.175	3948	0.177	4077	0.972	0.983	99.9509	0.173
2.953-3.156	0.18	100	0.168	3767	0.168	3872	0.984	0.985	99.8709	0.17
3.156-3.408	0.198	96	0.163	3503	0.164	3601	0.979	0.986	99.9445	0.171
3.408-3.731	0.18	71	0.164	3229	0.164	3303	0.981	0.987	99.9092	0.176
3.731-4.169	0.159	77	0.138	2929	0.138	3008	0.983	0.99	99.9335	0.159
4.169-4.807	0.132	58	0.121	2569	0.121	2630	0.992	0.992	99.8859	0.151
4.807-5.873	0.188	78	0.134	2178	0.136	2265	0.983	0.991	99.6027	0.164
5.873-8.244	0.191	16	0.154	1735	0.154	1758	0.981	0.988	99.6018	0.196
8.244-47.717	0.222	15	0.151	983	0.152	1017	0.979	0.986	98.1318	0.204

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	1.7091	-0.0344	0.083	1.6755	0.3841	1.6683	-0.0524	0.0967	0.3254	-0.2188	-0.0348	0.3201	-0.233	-0.2228	0.0872	0.1697	0.0036	0.0515	0.108	-0.017	0.2827	6.0607	7.6442	18.6862
2	1.7838	0.3905	-0.3021	1.8791	0.0433	1.4376	-0.083	0.1654	-0.1121	-0.0724	-0.0197	0.2626	0.1252	-0.1717	0.1028	0.1337	-0.0759	0.1384	0.0768	-0.0784	0.2253	4.617	-25.9806	20.6596
3	1.8132	-0.0861	-0.1661	2.3585	0.2838	1.7557	-0.0495	0.5887	-0.0368	-0.6741	-0.0157	0.0142	-0.045	-0.0356	0.0652	0.3528	-0.0847	0.128	0.2934	-0.036	0.1217	21.9033	-11.301	-4.2064
4	0.9343	0.4482	-0.1365	1.7681	0.4556	1.2983	-0.0346	0.002	0.1296	0.001	0.0367	0.0345	-0.0731	-0.0106	-0.0021	0.1378	-0.0311	0.1393	0.0122	-0.0346	0.189	27.8189	8.8839	29.5815
5	1.0694	0.0438	-0.2831	1.9054	-0.4957	0.9837	-0.0136	-0.0207	-0.0793	0.1762	-0.0237	-0.0953	0.0264	0.0646	0.0373	0.1742	-0.0328	0.141	0.0155	-0.0309	0.158	22.9096	-23.4757	36.7359
6	1.6569	-0.3038	-0.6733	1.4137	0.3661	1.42	-0.0694	0.1276	-0.0171	-0.1701	0.0092	-0.2158	0.0553	0.1677	0.0602	0.219	-0.0562	0.2242	0.1563	-0.042	0.2333	41.3534	-14.9216	10.054

Refinement TLS group

Selection: ALL

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