PDB-9k6k: monkeypox thymidine kinase

ID or keywords:

Entry

Database: PDB / ID: 9k6k

Title

monkeypox thymidine kinase

Components

Thymidine kinase

Keywords

VIRAL PROTEIN / complex / kinase

Function / homology

Function and homology information

thymidine metabolic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / ATP binding / metal ion binding
Similarity search - Function

Biological species

Monkeypox virus

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.826 Å

Authors

Zhang, T. / Cui, W. / Wang, W.

Funding support

China, 1items

Citation

Journal: Antiviral Res. / Year: 2025
Title: Structural and mechanistic insight into the phosphorylation reaction catalyzed by mpox virus thymidine kinase.
Authors: Zhang, T. / Chen, X. / Tao, C. / Huang, H. / Luo, Z. / Liu, M. / Cui, W. / Wang, W.

History

Deposition	Oct 22, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9k6k.cif.gz	249.7 KB	Display	PDBx/mmCIF format
PDB format	pdb9k6k.ent.gz	202.3 KB	Display	PDB format
PDBx/mmJSON format	9k6k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9k6k_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	9k6k_full_validation.pdf.gz	2.5 MB	Display
Data in XML	9k6k_validation.xml.gz	25.5 KB	Display
Data in CIF	9k6k_validation.cif.gz	32.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k6/9k6k ftp://data.pdbj.org/pub/pdb/validation_reports/k6/9k6k	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	#238 - Oct 2019 Ribonucleotide Reductase similarity (1)

Deposited unit

A: Thymidine kinase

B: Thymidine kinase

C: Thymidine kinase

D: Thymidine kinase

hetero molecules

81.1 kDa, 4 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)	94.272, 63.762, 117.106
Angle α, β, γ (deg.)	90.00, 111.16, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Thymidine kinase Mass: 20019.203 Da / Num. of mol.: 4 / Mutation: E83A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus / Gene: OPG101, TK, MPXV084 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H0DN73, thymidine kinase
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₂O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	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: 2.04 Å³/Da / Density % sol: 39.81 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / Details: PEG 400, potassium phosphate

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Data collection

Diffraction	Mean temperature: 193 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.826→109.21 Å / Num. obs: 15394 / % possible obs: 97.9 % / Redundancy: 4.3 % / CC_1/2: 0.994 / R_merge(I) obs: 0.096 / R_pim(I) all: 0.073 / R_rim(I) all: 0.121 / Net I/σ(I): 8.5
Reflection shell	Resolution: 2.83→2.98 Å / R_merge(I) obs: 0.634 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2131 / CC_1/2: 0.756 / R_pim(I) all: 0.524 / R_rim(I) all: 0.826

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data scaling
XDS		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.826→31.881 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.88 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2639	708	4.61 %
R_work	0.2248	-	-
obs	0.2265	15372	97.6 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.826→31.881 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4507	0	47	0	4554

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4612
X-RAY DIFFRACTION	f_angle_d	0.697	6234
X-RAY DIFFRACTION	f_dihedral_angle_d	15.779	1656
X-RAY DIFFRACTION	f_chiral_restr	0.05	736
X-RAY DIFFRACTION	f_plane_restr	0.004	783

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 (%)
2.826-3.0437	0.3519	131	0.2917	2821	X-RAY DIFFRACTION	94
3.0437-3.3497	0.3145	157	0.2526	2928	X-RAY DIFFRACTION	98
3.3497-3.8337	0.2824	142	0.234	2910	X-RAY DIFFRACTION	98
3.8337-4.8274	0.2347	142	0.2092	2952	X-RAY DIFFRACTION	98
4.8274-31.881	0.2497	136	0.2135	3053	X-RAY DIFFRACTION	99

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	1.1179	0.493	0.2856	0.8895	0.3613	0.7348	-0.3051	-0.1781	0.6413	-0.1859	-0.0952	-0.2023	-0.0758	-0.137	-0.3883	0.3977	-0.4561	-0.2308	0.7715	0.1411	0.614	23.4891	11.8967	21.1552
2	2.958	0.6172	0.5184	4.2853	0.0869	2.3245	0.1534	-0.5233	0.3589	0.7673	-0.2232	-0.6382	-0.1134	0.2671	0.3263	0.7023	-0.4448	-0.0161	0.6553	0.1095	0.8712	33.1749	14.9074	18.523
3	1.5751	1.7526	-0.0661	2.6564	-0.4742	0.2539	0.0155	0.0609	-0.418	-0.0727	0.0362	-0.5523	0.0171	0.0814	1.8397	0.6447	-1.0283	0.2526	0.8925	-0.0122	0.6357	34.9251	14.9734	7.668
4	6.6283	3.0561	0.6463	6.5743	-0.4115	4.3575	-0.3947	1.0367	0.0527	-0.5552	-0.0642	-0.5331	-0.0531	0.6307	0.4042	0.4323	-0.2924	0.0614	0.5853	0.0078	0.7192	31.7019	11.848	13.1906
5	1.2241	-0.3808	2.0263	2.9632	0.6412	3.9283	0.3294	0.56	-0.5425	0.2332	-0.082	-1.2157	0.1146	0.9157	0.4952	0.3807	-0.4125	0.1327	0.8438	-0.091	0.8258	31.7559	4.325	12.3064
6	7.5649	4.9956	1.5383	7.5235	3.786	2.1291	-0.2228	2.1269	0.4086	-0.3348	0.4067	0.9016	0.9595	-1.1041	0.1019	0.6776	-0.3948	-0.0719	1.1105	0.2497	0.8163	12.3061	10.376	4.4969
7	4.9733	-0.992	-1.4629	5.8257	0.1648	1.4308	0.0372	0.7753	0.0766	-0.8002	0.0553	0.7632	-0.003	-0.1887	0.014	0.8058	-0.4475	-0.0716	0.9241	0.0892	0.7142	12.4759	9.0194	14.1887
8	4.364	-0.0584	-0.9901	5.5288	-3.6885	6.7663	-0.5699	0.6505	1.7503	-0.3194	0.1031	0.553	-0.5389	-0.5841	0.545	0.669	-0.2951	-0.1873	1.4922	0.2261	1.1147	8.4361	21.6667	5.6119
9	4.307	3.3583	-2.9124	6.6788	0.9872	4.5898	-0.2585	1.1021	0.6206	-0.8136	-0.8192	-0.2137	-0.9516	0.2541	0.7338	0.6803	-0.1553	-0.0705	0.9313	0.1895	0.6723	1.251	15.9755	7.9406
10	1.2277	0.01	1.6153	5.053	-0.4988	2.2299	-0.319	-0.674	-0.3253	0.7915	0.0383	0.2444	0.1526	-0.5933	-0.2535	0.3912	-0.284	0.0278	0.6	0.0221	0.6599	1.8276	-5.3595	20.9233
11	8.1451	1.8549	0.011	6.4141	-6.4059	9.0504	-0.0757	1.1338	-0.9778	-0.7103	-0.2728	-1.3442	0.6458	1.0775	0.6499	0.4411	-0.347	0.0424	0.7264	-0.1287	0.94	0.9658	-17.0836	10.4034
12	8.3597	-0.3688	-0.4131	4.1923	1.8269	4.137	0.0162	1.6701	-0.0905	-0.6551	0.0832	1.2645	-0.451	-0.6049	0.1124	0.5813	-0.4578	0.0048	0.9454	0.0157	0.92	-1.4894	-5.0455	10.0238
13	8.8271	3.1898	2.6038	5.5168	-0.2965	1.8375	-0.38	1.0864	-0.4413	-0.4463	0.3263	1.0445	-0.0942	0.2286	0.4886	0.6872	-0.4318	0.2153	0.9796	-0.2663	1.1957	18.4626	-8.787	9.0171
14	5.591	-0.6868	0.909	3.8846	-1.6092	3.562	-0.3691	0.5179	-0.3973	-0.1211	-0.2643	-0.6093	0.4475	0.3704	0.5907	0.4094	-0.2907	0.1181	0.7135	0.0478	0.6773	18.2567	-5.297	18.6876
15	2.3084	-0.5955	4.079	6.4591	-2.6693	7.6118	0.2088	0.352	-0.0761	-0.9746	-0.2634	-2.2165	1.5508	0.7934	-0.2469	1.0764	0.006	0.2551	0.476	-0.2048	1.973	20.527	-22.3194	13.5896
16	3.0666	2.3231	-4.5041	8.0757	-3.6481	6.6098	-0.1452	0.152	-2.169	-0.1577	-0.3757	-0.7395	0.1556	0.5338	0.3351	0.5651	-0.2814	-0.0033	0.7866	0.1044	1.182	28.6625	-11.9211	18.7141
17	7.9566	-1.7005	2.2288	3.3567	-1.9051	3.9376	-0.068	-0.0814	1.0274	0.4392	-0.2535	0.3434	0.219	0.2284	0.2603	0.6415	-0.2252	0.1159	0.6799	-0.0185	0.7715	12.3479	18.4959	29.4226
18	8.0076	4.2473	4.2189	6.8667	5.0719	7.5142	0.291	-0.433	1.6463	0.1309	-0.2318	0.4714	-0.8662	-0.1526	0.2695	0.7369	-0.1481	0.0783	0.665	-0.3255	1.3031	9.3411	30.5496	34.804
19	3.8701	-3.8619	-3.8715	9.2398	0.0008	6.6448	0.3301	-0.3116	0.3823	0.1192	-0.233	1.3334	-1.9113	-0.5993	0.1379	1.0609	0.1691	-0.0985	0.9238	-0.6118	1.6439	1.1101	33.1607	33.8493
20	2.0992	1.4961	2.104	6.2175	-0.0795	8.241	0.1482	-1.7472	1.6292	1.2532	-0.2665	0.6339	-1.3888	-0.4219	0.1673	1.0059	-0.1574	0.1428	0.9345	-0.237	0.9239	6.0387	23.1565	38.652
21	2.6928	-1.1826	0.2195	2.4712	1.3307	2.5425	-0.2512	-0.5884	0.2468	0.8551	0.2134	-0.1462	0.1434	0.0865	-0.2775	1.1852	-0.4269	0.1394	0.701	-0.4313	0.3054	17.7021	14.7761	47.1662
22	4.1468	-0.4006	-1.1362	2.3697	2.3308	2.6779	0.1242	-1.2989	-0.1202	0.9904	0.1259	-0.5638	0.4582	1.1052	-0.3404	0.8642	-0.4442	-0.0863	0.9007	0.0329	0.5392	23.0234	9.8882	39.7205
23	2.7644	-0.7785	0.5603	5.712	0.8081	3.4343	0.2098	-0.6017	-0.4665	1.0947	-0.6458	0.0159	-0.0266	-0.4387	0.438	0.6316	-0.3282	-0.0007	0.9425	0.1669	0.7467	12.181	-7.7352	35.7342
24	0.3446	-0.068	0.5239	0.8505	0.3935	1.0796	-0.1702	-0.5979	-0.3856	1.1644	-0.6266	-0.5002	0.6861	0.6041	-0.4976	1.1588	-0.3391	-0.0206	1.5331	0.6671	1.0584	13.6396	-13.9845	50.1417
25	5.5913	-0.3366	-2.0825	3.7643	-1.3891	1.3862	0.4262	-3.1263	-0.6801	1.5378	0.0058	0.2398	-0.2257	-0.0944	0.2137	1.2157	-0.4254	0.0171	1.4966	0.3862	0.7484	14.282	-4.9814	47.0214
26	6.1027	-4.0546	3.3841	8.3189	1.5823	4.4823	-0.2667	-3.2877	-1.1343	1.9444	-0.7867	0.9513	0.5673	0.1444	0.7058	1.4506	-0.4103	0.2058	1.6308	0.1892	1.2273	1.8502	5.4283	47.3233
27	2.9439	-2.8502	1.5774	6.9229	-3.0726	5.3294	-0.0077	-2.2418	0.1178	0.6659	0.3341	-0.2162	-0.3945	0.8926	-0.2471	0.889	-0.2847	0.0075	1.2939	0.0008	0.5209	13.7892	4.7034	41.2944
28	8.638	-5.0352	4.0238	6.2829	1.4234	6.2675	0.5372	0.9639	0.5171	-0.1858	0.0349	1.5374	0.3613	-0.6583	-0.6286	0.5336	-0.2811	0.0526	0.968	0.0673	0.724	-6.1949	5.8357	29.587
29	4.3443	-0.6736	0.5819	2.2241	-0.4777	0.3389	-0.153	-0.2093	0.2596	0.0342	-0.3283	-0.0767	0.1175	0.7114	-2.1567	0.6348	-0.2389	0.5749	1.1803	-0.1025	1.0103	-7.5333	5.1144	38.1756
30	2.4667	-2.469	0.613	7.8159	-4.6427	3.2109	-0.0835	-1.0895	0.8441	0.8947	-1.0938	1.2193	-0.1758	-1.9252	0.412	0.9263	-0.0423	0.1589	1.3872	-0.1707	1.4859	-9.5471	13.8145	36.6095

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 40 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 41 through 71 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 72 through 87 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 88 through 107 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 108 through 118 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 119 through 146 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 147 through 165 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 166 through 177 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 40 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 41 through 68 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 69 through 107 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 121 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 122 through 150 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 151 through 165 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 166 through 176 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 2 through 31 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 32 through 68 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 69 through 77 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 78 through 107 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 108 through 121 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 122 through 174 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 4 through 39 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 40 through 77 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 78 through 107 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 108 through 121 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 122 through 134 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 135 through 146 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 147 through 170 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 171 through 176 )

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Yorodumi