PDB-9h6p: Crystal structure of NUDT14 complexed with novel compound AMNUDT1...

ID or keywords:

Entry

Database: PDB / ID: 9h6p

Title

Crystal structure of NUDT14 complexed with novel compound AMNUDT14-003 in spacegroup P1

Components

Uridine diphosphate glucose pyrophosphatase NUDT14

Keywords

HYDROLASE / nudix domain / Structural Genomics / Structural Genomics Consortium / SGC

Function / homology

Function and homology information

Synthesis of dolichyl-phosphate-glucose / UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / protein N-linked glycosylation via asparagine / metal ion binding / identical protein binding / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.162 Å

Authors

Balikci, E. / Koekemoer, L. / Dlamini, L.S. / Gurav, N. / Apostolidou, M. / Adcock, C. / McGown, A. / Marques, A.M.C. / Spencer, J. / Huber, K.V.M. / Structural Genomics Consortium (SGC)

Funding support

Switzerland, 1items

Citation

Journal: To Be Published
Title: Crystal structure of NUDT14 complexed with novel compound AMNUDT14-003 in spacegroup
Authors: Balikci, E. / Koekemoer, L. / Dlamini, L.S. / Gurav, N. / Apostolidou, M. / Adcock, C. / McGown, A. / Marques, A.M.C. / Spencer, J. / Huber, K.V.M.

History

Deposition	Oct 24, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9h6p.cif.gz	338.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9h6p.ent.gz		Display	PDB format
PDBx/mmJSON format	9h6p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9h6p_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	9h6p_full_validation.pdf.gz	1.4 MB	Display
Data in XML	9h6p_validation.xml.gz	65.1 KB	Display
Data in CIF	9h6p_validation.cif.gz	82.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h6/9h6p ftp://data.pdbj.org/pub/pdb/validation_reports/h6/9h6p	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	#145 - Jan 2012 Messenger RNA Capping similarity (3) #201 - Sep 2016 Isoprene Synthase similarity (3)

Deposited unit

A: Uridine diphosphate glucose pyrophosphatase NUDT14

B: Uridine diphosphate glucose pyrophosphatase NUDT14

C: Uridine diphosphate glucose pyrophosphatase NUDT14

D: Uridine diphosphate glucose pyrophosphatase NUDT14

E: Uridine diphosphate glucose pyrophosphatase NUDT14

F: Uridine diphosphate glucose pyrophosphatase NUDT14

G: Uridine diphosphate glucose pyrophosphatase NUDT14

H: Uridine diphosphate glucose pyrophosphatase NUDT14

hetero molecules

195 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uridine diphosphate glucose pyrophosphatase NUDT14

E: Uridine diphosphate glucose pyrophosphatase NUDT14

hetero molecules

defined by author
Evidence: gel filtration
48.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Uridine diphosphate glucose pyrophosphatase NUDT14

D: Uridine diphosphate glucose pyrophosphatase NUDT14

hetero molecules

defined by author
48.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Uridine diphosphate glucose pyrophosphatase NUDT14

F: Uridine diphosphate glucose pyrophosphatase NUDT14

hetero molecules

defined by author
48.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Uridine diphosphate glucose pyrophosphatase NUDT14

H: Uridine diphosphate glucose pyrophosphatase NUDT14

hetero molecules

defined by author
48.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.886, 85.392, 106.742
Angle α, β, γ (deg.)	89.955, 89.998, 78.77
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 1 - 220 / Label seq-ID: 1 - 220

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
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56

#1: Protein	Uridine diphosphate glucose pyrophosphatase NUDT14 / UDPG pyrophosphatase / UGPPase / Nucleoside diphosphate-linked moiety X motif 14 / Nudix motif 14 / ...UDPG pyrophosphatase / UGPPase / Nucleoside diphosphate-linked moiety X motif 14 / Nudix motif 14 / Nudix Hydrolase 14 Mass: 24141.211 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT14, UGPP / Production host: Escherichia coli (E. coli) / References: UniProt: O95848, UDP-sugar diphosphatase
#2: Chemical	ChemComp-A1ISQ / 3-(1H-indol-6-yl)-1-(1-methylpiperidin-4-yl)pyrazolo[3,4-d]pyrimidin-4-amine Mass: 347.417 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₉H₂₁N₇ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.49 Å³/Da / Density % sol: 50.69 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: Hampton Crystal Screen condition A09 30% PEG4000 0.2M ammonium acetate 0.1M citrate pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 8, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 3.162→106.742 Å / Num. obs: 12794 / % possible obs: 85.2 % / Redundancy: 3.6 % / CC_1/2: 0.981 / Net I/σ(I): 3.2
Reflection shell	Resolution: 3.162→3.666 Å / Num. unique obs: 640 / CC_1/2: 0.819

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.88)	refinement
autoPROC		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.162→106.742 Å / Cor.coef. F_o:F_c: 0.904 / Cor.coef. F_o:F_c free: 0.838 / WR_factor R_free: 0.258 / WR_factor R_work: 0.205 / SU B: 38.885 / SU ML: 0.645 / Average fsc free: 0.9531 / Average fsc work: 0.9698 / Cross valid method: FREE R-VALUE / ESU R Free: 1.195 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2652	644	5.034 %
R_work	0.211	12150	-
all	0.214	-	-
obs	-	12794	40.137 %

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: 47.576 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.703 Å²	-0.791 Å²	0.286 Å²
2-	-	-0.478 Å²	0.034 Å²
3-	-	-	1.905 Å²

Refinement step

Cycle: LAST / Resolution: 3.162→106.742 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12850	0	104	11	12965

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	13265
X-RAY DIFFRACTION	r_angle_refined_deg	1.357	1.816	18051
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.036	5	1653
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.104	5	117
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.084	10	2053
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	12.28	10	584
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	1988
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10340
X-RAY DIFFRACTION	r_nbd_refined	0.235	0.2	6224
X-RAY DIFFRACTION	r_nbtor_refined	0.308	0.2	9047
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.159	0.2	559
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.409	0.2	173
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.426	0.2	10
X-RAY DIFFRACTION	r_mcbond_it	3.431	4.644	6669
X-RAY DIFFRACTION	r_mcangle_it	6.095	8.332	8303
X-RAY DIFFRACTION	r_scbond_it	3.254	4.846	6596
X-RAY DIFFRACTION	r_scangle_it	5.76	8.811	9748
X-RAY DIFFRACTION	r_lrange_it	12.135	63.932	20125
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.056	0.05	6496
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.051	0.05	6421
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.075	0.05	6071
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.07	0.05	6089
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.075	0.05	6184
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.061	0.05	6390
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.093	0.05	6298
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.047	0.05	6442
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.078	0.05	6057
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.072	0.05	6082
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.063	0.05	6193
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.054	0.05	6399
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.085	0.05	6301
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.064	0.05	6043
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.071	0.05	6088
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.059	0.05	6193
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.045	0.05	6458
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.081	0.05	6310
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.074	0.05	6046
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.073	0.05	6063
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.074	0.05	6017
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.087	0.05	6038
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.067	0.05	6065
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.073	0.05	6077
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.084	0.05	6079
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.068	0.05	6164
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.084	0.05	6222
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.078	0.05	6314

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	0.05646	0.0501
1	2	B	X-RAY DIFFRACTION	Local ncs	0.05646	0.0501
2	3	A	X-RAY DIFFRACTION	Local ncs	0.05061	0.0501
2	4	C	X-RAY DIFFRACTION	Local ncs	0.05061	0.0501
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07467	0.0501
3	6	D	X-RAY DIFFRACTION	Local ncs	0.07467	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.06955	0.0501
4	8	E	X-RAY DIFFRACTION	Local ncs	0.06955	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07467	0.0501
5	10	F	X-RAY DIFFRACTION	Local ncs	0.07467	0.0501
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06091	0.0501
6	12	G	X-RAY DIFFRACTION	Local ncs	0.06091	0.0501
7	13	A	X-RAY DIFFRACTION	Local ncs	0.09272	0.0501
7	14	H	X-RAY DIFFRACTION	Local ncs	0.09272	0.0501
8	15	B	X-RAY DIFFRACTION	Local ncs	0.04674	0.0501
8	16	C	X-RAY DIFFRACTION	Local ncs	0.04674	0.0501
9	17	B	X-RAY DIFFRACTION	Local ncs	0.07828	0.0501
9	18	D	X-RAY DIFFRACTION	Local ncs	0.07828	0.0501
10	19	B	X-RAY DIFFRACTION	Local ncs	0.07177	0.0501
10	20	E	X-RAY DIFFRACTION	Local ncs	0.07177	0.0501
11	21	B	X-RAY DIFFRACTION	Local ncs	0.06335	0.0501
11	22	F	X-RAY DIFFRACTION	Local ncs	0.06335	0.0501
12	23	B	X-RAY DIFFRACTION	Local ncs	0.05389	0.0501
12	24	G	X-RAY DIFFRACTION	Local ncs	0.05389	0.0501
13	25	B	X-RAY DIFFRACTION	Local ncs	0.08492	0.0501
13	26	H	X-RAY DIFFRACTION	Local ncs	0.08492	0.0501
14	27	C	X-RAY DIFFRACTION	Local ncs	0.0642	0.0501
14	28	D	X-RAY DIFFRACTION	Local ncs	0.0642	0.0501
15	29	C	X-RAY DIFFRACTION	Local ncs	0.07117	0.0501
15	30	E	X-RAY DIFFRACTION	Local ncs	0.07117	0.0501
16	31	C	X-RAY DIFFRACTION	Local ncs	0.05924	0.0501
16	32	F	X-RAY DIFFRACTION	Local ncs	0.05924	0.0501
17	33	C	X-RAY DIFFRACTION	Local ncs	0.04505	0.0501
17	34	G	X-RAY DIFFRACTION	Local ncs	0.04505	0.0501
18	35	C	X-RAY DIFFRACTION	Local ncs	0.08139	0.0501
18	36	H	X-RAY DIFFRACTION	Local ncs	0.08139	0.0501
19	37	D	X-RAY DIFFRACTION	Local ncs	0.07381	0.0501
19	38	E	X-RAY DIFFRACTION	Local ncs	0.07381	0.0501
20	39	D	X-RAY DIFFRACTION	Local ncs	0.07336	0.0501
20	40	F	X-RAY DIFFRACTION	Local ncs	0.07336	0.0501
21	41	D	X-RAY DIFFRACTION	Local ncs	0.07437	0.0501
21	42	G	X-RAY DIFFRACTION	Local ncs	0.07437	0.0501
22	43	D	X-RAY DIFFRACTION	Local ncs	0.08697	0.0501
22	44	H	X-RAY DIFFRACTION	Local ncs	0.08697	0.0501
23	45	E	X-RAY DIFFRACTION	Local ncs	0.06716	0.0501
23	46	F	X-RAY DIFFRACTION	Local ncs	0.06716	0.0501
24	47	E	X-RAY DIFFRACTION	Local ncs	0.07326	0.0501
24	48	G	X-RAY DIFFRACTION	Local ncs	0.07326	0.0501
25	49	E	X-RAY DIFFRACTION	Local ncs	0.08407	0.0501
25	50	H	X-RAY DIFFRACTION	Local ncs	0.08407	0.0501
26	51	F	X-RAY DIFFRACTION	Local ncs	0.06807	0.0501
26	52	G	X-RAY DIFFRACTION	Local ncs	0.06807	0.0501
27	53	F	X-RAY DIFFRACTION	Local ncs	0.08425	0.0501
27	54	H	X-RAY DIFFRACTION	Local ncs	0.08425	0.0501
28	55	G	X-RAY DIFFRACTION	Local ncs	0.07816	0.0501
28	56	H	X-RAY DIFFRACTION	Local ncs	0.07816	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 work	% reflection obs (%)	WR_factor R_work	Fsc free
3.162-3.244	0.246	1	0.282	27	0.28	2310	0.967	1.2121	0.289
3.244-3.333	0.164	3	0.259	60	0.254	2341	0.964	2.6912	0.247	0.98
3.333-3.429	0.137	4	0.269	89	0.261	2214	0.95	4.2005	0.262	0.988
3.429-3.535	0.417	7	0.25	145	0.256	2189	0.962	6.9438	0.249	0.787
3.535-3.651	0.317	11	0.284	252	0.285	2082	0.95	12.6321	0.282	0.889
3.651-3.779	0.229	27	0.268	403	0.266	2018	0.947	21.3082	0.261	0.972
3.779-3.921	0.392	26	0.241	558	0.247	2001	0.963	29.1854	0.231	0.895
3.921-4.081	0.301	30	0.241	670	0.243	1875	0.964	37.3333	0.235	0.928
4.081-4.262	0.313	36	0.23	784	0.234	1818	0.967	45.1045	0.216	0.947
4.262-4.47	0.249	39	0.181	818	0.183	1733	0.979	49.4518	0.168	0.967
4.47-4.711	0.246	33	0.195	902	0.197	1642	0.976	56.9428	0.181	0.966
4.711-4.996	0.274	47	0.208	895	0.212	1564	0.973	60.2302	0.194	0.957
4.996-5.34	0.273	61	0.194	899	0.198	1459	0.977	65.7985	0.178	0.967
5.34-5.767	0.281	54	0.229	946	0.232	1362	0.967	73.4214	0.211	0.963
5.767-6.316	0.313	57	0.248	1003	0.252	1255	0.963	84.4622	0.235	0.941
6.316-7.058	0.311	68	0.241	1029	0.245	1152	0.965	95.2257	0.226	0.951
7.058-8.144	0.228	48	0.203	921	0.205	982	0.974	98.6762	0.195	0.967
8.144-9.96	0.181	47	0.15	802	0.152	857	0.988	99.0665	0.151	0.978
9.96-14.024	0.186	28	0.154	618	0.155	658	0.986	98.1763	0.167	0.99
14.024-106.742	0.353	17	0.304	328	0.307	362	0.938	95.3039	0.356	0.948

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