PDB-8qw1: Human NDPK-C in complex with ADP and Mg2+

ID or keywords:

Entry

Database: PDB / ID: 8qw1

Title

Human NDPK-C in complex with ADP 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 / nucleoside diphosphate kinase activity / GTP biosynthetic process / mitochondrial outer membrane / ciliary basal body ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 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	8qw1.cif.gz	502.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8qw1.ent.gz	316.2 KB	Display	PDB format
PDBx/mmJSON format	8qw1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8qw1_validation.pdf.gz	4.5 MB	Display	wwPDB validaton report
Full document	8qw1_full_validation.pdf.gz	4.5 MB	Display
Data in XML	8qw1_validation.xml.gz	44.2 KB	Display
Data in CIF	8qw1_validation.cif.gz	57.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qw/8qw1 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/8qw1	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	#233 - May 2019 S-Nitrosylated Hemoglobin similarity (1) #238 - Oct 2019 Ribonucleotide Reductase 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)	106.460, 116.310, 84.070
Angle α, β, γ (deg.)	90.000, 93.054, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	F-332- 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-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*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.: 399 / 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: 2.47 Å³/Da / Density % sol: 50.3 %
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: ID23-2 / Wavelength: 0.8731 Å
Detector	Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 7, 2021 / Details: KB mirror
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 2.1→42.011 Å / Num. obs: 57087 / % possible obs: 95.8 % / Redundancy: 6.6 % / B_iso Wilson estimate: 41.6 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.184 / R_rim(I) all: 0.199 / Net I/σ(I): 10.01
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 5.9 % / R_merge(I) obs: 1.509 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 3195 / CC_1/2: 0.466 / R_rim(I) all: 1.659 / % possible all: 73.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→42.011 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.953 / SU B: 11.137 / SU ML: 0.137 / Cross valid method: FREE R-VALUE / ESU R: 0.216 / ESU R Free: 0.167
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2045	2382	4.173 %
R_work	0.1722	54705	-
all	0.174	-	-
obs	-	57087	95.821 %

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: 39.151 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.344 Å²	-0 Å²	0.735 Å²
2-	-	-0.853 Å²	-0 Å²
3-	-	-	0.429 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→42.011 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7284	0	168	399	7851

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	7224
X-RAY DIFFRACTION	r_angle_refined_deg	1.641	1.67	10446
X-RAY DIFFRACTION	r_angle_other_deg	0.516	1.581	16524
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.469	5	906
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.875	5	96
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.131	5	6
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.973	10	1266
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.579	10	360
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1116
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	9192
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1902
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1411
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	6725
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	3698
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	4154
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	399
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.049	0.2	4
X-RAY DIFFRACTION	r_metal_ion_refined	0.061	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.203	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.198	0.2	69
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.075	0.2	18
X-RAY DIFFRACTION	r_mcbond_it	2.654	2.661	3642
X-RAY DIFFRACTION	r_mcbond_other	2.653	2.662	3642
X-RAY DIFFRACTION	r_mcangle_it	3.737	4.828	4578
X-RAY DIFFRACTION	r_mcangle_other	3.718	4.766	4543
X-RAY DIFFRACTION	r_scbond_it	4.283	3.259	3978
X-RAY DIFFRACTION	r_scbond_other	4.283	3.259	3978
X-RAY DIFFRACTION	r_scangle_it	6.525	5.819	5886
X-RAY DIFFRACTION	r_scangle_other	6.526	5.818	5883
X-RAY DIFFRACTION	r_lrange_it	7.94	27.416	8575
X-RAY DIFFRACTION	r_lrange_other	7.927	26.974	8524
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.071	0.05	4881
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.074	0.05	4862
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.07	0.05	4884
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.075	0.05	4845
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.072	0.05	4865
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.064	0.05	4902
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.072	0.05	4854
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.07	0.05	4864
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.062	0.05	4896
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.07	0.05	4835
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.073	0.05	4864
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.069	0.05	4871
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.071	0.05	4889
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.066	0.05	4896
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.051	0.05	4928

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	0.07097	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07097	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07371	0.0501
2	4	A	X-RAY DIFFRACTION	Local ncs	0.07371	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.06951	0.0501
3	6	A	X-RAY DIFFRACTION	Local ncs	0.06951	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0749	0.0501
4	8	A	X-RAY DIFFRACTION	Local ncs	0.0749	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07212	0.0501
5	10	A	X-RAY DIFFRACTION	Local ncs	0.07212	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.0638	0.0501
6	12	A	X-RAY DIFFRACTION	Local ncs	0.0638	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.07237	0.0501
7	14	A	X-RAY DIFFRACTION	Local ncs	0.07237	0.0501
8	15	A	X-RAY DIFFRACTION	Local ncs	0.06997	0.0501
8	16	A	X-RAY DIFFRACTION	Local ncs	0.06997	0.0501
9	17	A	X-RAY DIFFRACTION	Local ncs	0.0618	0.0501
9	18	A	X-RAY DIFFRACTION	Local ncs	0.0618	0.0501
10	19	A	X-RAY DIFFRACTION	Local ncs	0.07032	0.0501
10	20	A	X-RAY DIFFRACTION	Local ncs	0.07032	0.0501
11	21	A	X-RAY DIFFRACTION	Local ncs	0.07315	0.0501
11	22	A	X-RAY DIFFRACTION	Local ncs	0.07315	0.0501
12	23	A	X-RAY DIFFRACTION	Local ncs	0.06869	0.0501
12	24	A	X-RAY DIFFRACTION	Local ncs	0.06869	0.0501
13	25	A	X-RAY DIFFRACTION	Local ncs	0.07107	0.0501
13	26	A	X-RAY DIFFRACTION	Local ncs	0.07107	0.0501
14	27	A	X-RAY DIFFRACTION	Local ncs	0.06639	0.0501
14	28	A	X-RAY DIFFRACTION	Local ncs	0.06639	0.0501
15	29	A	X-RAY DIFFRACTION	Local ncs	0.05087	0.0501
15	30	A	X-RAY DIFFRACTION	Local ncs	0.05087	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
2.1-2.154	0.348	140	0.321	3049	0.322	4366	0.929	0.942	73.0417	0.29
2.154-2.213	0.296	131	0.292	3469	0.292	4294	0.956	0.951	83.8379	0.254
2.213-2.277	0.374	148	0.307	3886	0.309	4134	0.894	0.942	97.581	0.266
2.277-2.347	0.296	155	0.241	3850	0.243	4055	0.943	0.964	98.767	0.209
2.347-2.424	0.272	170	0.218	3684	0.221	3896	0.955	0.972	98.922	0.187
2.424-2.509	0.245	160	0.196	3576	0.198	3778	0.963	0.978	98.8883	0.169
2.509-2.603	0.229	171	0.19	3442	0.192	3648	0.968	0.979	99.0406	0.162
2.603-2.709	0.223	163	0.174	3348	0.177	3541	0.973	0.982	99.1528	0.15
2.709-2.829	0.22	167	0.175	3177	0.178	3369	0.975	0.982	99.2579	0.154
2.829-2.966	0.2	128	0.168	3066	0.17	3215	0.975	0.985	99.3468	0.15
2.966-3.126	0.2	110	0.16	2960	0.161	3086	0.98	0.987	99.4815	0.147
3.126-3.314	0.204	109	0.169	2799	0.171	2924	0.976	0.985	99.4528	0.161
3.314-3.541	0.191	104	0.165	2608	0.166	2725	0.982	0.987	99.5229	0.159
3.541-3.823	0.181	103	0.155	2431	0.156	2550	0.983	0.988	99.3726	0.152
3.823-4.184	0.162	116	0.135	2231	0.136	2367	0.987	0.99	99.1551	0.138
4.184-4.672	0.149	125	0.115	2003	0.117	2135	0.988	0.993	99.6721	0.122
4.672-5.384	0.162	78	0.129	1798	0.131	1882	0.987	0.992	99.6812	0.136
5.384-6.567	0.184	50	0.158	1547	0.159	1614	0.982	0.988	98.9467	0.166
6.567-9.176	0.159	31	0.157	1202	0.157	1244	0.989	0.987	99.1158	0.172
9.176-42.011	0.286	23	0.213	579	0.215	745	0.95	0.978	80.8054	0.26

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	1.2089	0.0095	-0.0252	1.0617	0.3323	1.332	-0.0947	0.0523	0.2276	-0.1482	0.0037	0.2215	-0.1383	-0.1621	0.091	0.0439	0.0106	-0.0286	0.0742	0.0092	0.1432	5.859	7.5593	18.9458
2	1.1982	0.2737	-0.0564	1.4617	0.2142	1.0511	-0.0697	0.1014	-0.1385	-0.1077	0.0134	0.1718	0.0717	-0.1534	0.0563	0.0582	-0.0638	0.0428	0.1049	-0.0465	0.1191	4.59	-26.0842	20.794
3	0.9432	-0.1577	0.0975	1.4169	-0.1271	1.3058	-0.014	0.3935	-0.0446	-0.3233	-0.0452	0.0613	0.0399	-0.0319	0.0592	0.15	-0.0435	0.0249	0.2234	-0.0266	0.0283	21.7046	-11.1893	-4.0992
4	0.6579	0.5163	-0.1513	1.2483	0.2249	0.9094	-0.0275	-0.0332	0.1158	-0.0179	0.0303	0.0137	-0.0316	0.0381	-0.0028	0.042	-0.0229	0.0399	0.0512	-0.0263	0.0977	27.7528	8.8398	29.7407
5	0.7032	0.0177	-0.2145	1.312	-0.3717	0.994	0.0124	-0.034	-0.0718	0.1408	-0.0259	-0.0987	-0.0144	0.0009	0.0135	0.0678	-0.0178	0.0384	0.0509	0.0047	0.0706	22.9189	-23.5543	36.8521
6	1.2118	-0.3702	-0.4759	0.9563	0.1079	0.8318	-0.0495	0.0856	-0.0358	-0.067	-0.0345	-0.1115	0.0566	0.1205	0.0841	0.0896	-0.0213	0.0968	0.1456	-0.0005	0.1094	41.2847	-14.8442	10.1049

Refinement TLS group

Selection: ALL

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