PDB-9da6: Crystal structure of human DNPH1 bound to inhibitor 3a

ID or keywords:

Entry

Database: PDB / ID: 9da6

Title

Crystal structure of human DNPH1 bound to inhibitor 3a

Components

5-hydroxymethyl-dUMP N-hydrolase

Keywords

HYDROLASE/INHIBITOR / Inhibitor / Complex / HYDROLASE / HYDROLASE-INHIBITOR complex

Function / homology

Function and homology information

purine nucleotide catabolic process / deoxyribonucleoside monophosphate catabolic process / 5-hydroxymethyl-dUMP N-hydrolase activity / nucleoside salvage / dGMP catabolic process / Purine catabolism / allantoin metabolic process / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / epithelial cell differentiation / positive regulation of cell growth ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.35 Å

Authors

Wagner, A.G. / Schramm, V.L. / Almo, S.C. / Ghosh, A.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM041916	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	S10 OD020068	United States

Citation

Journal: J.Med.Chem. / Year: 2025
Title: Transition State Analogs of Human DNPH1 Reveal Two Electrophile Migration Mechanisms.
Authors: Wagner, A.G. / Lang, T.B.D. / Ledingham, E.T. / Ghosh, A. / Brooks, D. / Eskandari, R. / Suthagar, K. / Almo, S.C. / Lamiable-Oulaidi, F. / Tyler, P.C. / Schramm, V.L.

History

Deposition	Aug 21, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 5, 2025	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2025	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9da6.cif.gz	172.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9da6.ent.gz	138.4 KB	Display	PDB format
PDBx/mmJSON format	9da6.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9da6_validation.pdf.gz	936.4 KB	Display	wwPDB validaton report
Full document	9da6_full_validation.pdf.gz	937.8 KB	Display
Data in XML	9da6_validation.xml.gz	16.5 KB	Display
Data in CIF	9da6_validation.cif.gz	22.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/da/9da6 ftp://data.pdbj.org/pub/pdb/validation_reports/da/9da6	HTTPS FTP

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Related structure data

Related structure data	9da1C 9da2C 9da3C 9da4C 9da5C 4p5e 8qhq C: citing same article (ref.)
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

Deposited unit

A: 5-hydroxymethyl-dUMP N-hydrolase

B: 5-hydroxymethyl-dUMP N-hydrolase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, Superdex S200

Unit cell

Length a, b, c (Å)	62.749, 63.925, 127.407
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-320- HOH
2	1	A-423- HOH
3	1	B-371- HOH
4	1	B-391- HOH

#1: Protein	5-hydroxymethyl-dUMP N-hydrolase / 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 / c-Myc-responsive protein RCL Mass: 16224.247 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DNPH1, C6orf108, RCL / Plasmid: pET-28a(+) / Details (production host): LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL References: UniProt: O43598, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical	ChemComp-NR1 / (3R,4R)-3-hydroxy-4-[(phosphonooxy)methyl]pyrrolidinium Type: DNA linking / Mass: 198.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₃NO₅P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 243 / 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: 1.97 Å³/Da / Density % sol: 37.52 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% (w/v) PEG 3350, 0.2 M Sodium chloride and 0.1 M Bis-Tris

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.92 Å / Relative weight: 1
Reflection	Resolution: 1.35→22.56 Å / Num. obs: 56772 / % possible obs: 99.9 % / Redundancy: 9.4 % / CC_1/2: 1 / R_merge(I) obs: 0.041 / R_pim(I) all: 0.014 / R_rim(I) all: 0.043 / Χ²: 1.01 / Net I/σ(I): 22.7 / Num. measured all: 533085
Reflection shell	Resolution: 1.35→1.37 Å / % possible obs: 99.3 % / Redundancy: 9.1 % / R_merge(I) obs: 0.757 / Num. measured all: 25161 / Num. unique obs: 2757 / CC_1/2: 0.913 / R_pim(I) all: 0.262 / R_rim(I) all: 0.802 / Χ²: 1.09 / Net I/σ(I) obs: 2.9

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless		data scaling
PHASER		phasing
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.35→22.56 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.32 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1776	2923	5.16 %
R_work	0.1596	-	-
obs	0.1605	56700	99.89 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.35→22.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2074	0	28	243	2345

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008
X-RAY DIFFRACTION	f_angle_d	1.169
X-RAY DIFFRACTION	f_dihedral_angle_d	6.654	316
X-RAY DIFFRACTION	f_chiral_restr	0.077	317
X-RAY DIFFRACTION	f_plane_restr	0.025	389

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 (%)
1.35-1.37	0.2548	132	0.2471	2523	X-RAY DIFFRACTION	99
1.37-1.39	0.3007	141	0.2407	2557	X-RAY DIFFRACTION	100
1.39-1.42	0.2615	139	0.239	2506	X-RAY DIFFRACTION	100
1.42-1.45	0.2327	120	0.2208	2559	X-RAY DIFFRACTION	100
1.45-1.48	0.2145	142	0.1995	2498	X-RAY DIFFRACTION	100
1.48-1.51	0.2184	162	0.1947	2538	X-RAY DIFFRACTION	100
1.51-1.54	0.2373	130	0.1763	2567	X-RAY DIFFRACTION	100
1.54-1.58	0.203	145	0.1682	2510	X-RAY DIFFRACTION	100
1.58-1.62	0.1849	140	0.1622	2516	X-RAY DIFFRACTION	100
1.62-1.67	0.1876	121	0.1688	2575	X-RAY DIFFRACTION	100
1.67-1.73	0.1749	132	0.1599	2562	X-RAY DIFFRACTION	100
1.73-1.79	0.188	131	0.1611	2567	X-RAY DIFFRACTION	100
1.79-1.86	0.1665	146	0.1554	2543	X-RAY DIFFRACTION	100
1.86-1.94	0.1876	164	0.1653	2535	X-RAY DIFFRACTION	100
1.94-2.05	0.1683	133	0.1563	2548	X-RAY DIFFRACTION	100
2.05-2.17	0.1681	145	0.1558	2546	X-RAY DIFFRACTION	100
2.17-2.34	0.1542	130	0.1459	2600	X-RAY DIFFRACTION	100
2.34-2.58	0.2104	133	0.1575	2575	X-RAY DIFFRACTION	100
2.58-2.95	0.165	171	0.1599	2581	X-RAY DIFFRACTION	100
2.95-3.71	0.1739	135	0.1517	2636	X-RAY DIFFRACTION	100
3.71-22.56	0.1511	131	0.1471	2735	X-RAY DIFFRACTION	100

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	1.397	0.6384	-0.5417	4.4273	-0.7335	2.2232	0.0168	0.1854	0.1246	-0.1046	0.0006	-0.0078	-0.117	-0.021	-0.0344	0.0979	0.0276	-0.0114	0.1663	0.0228	0.1407	-14.6442	2.3619	-21.6049
2	3.4044	1.0446	-0.3812	2.4373	-0.2118	3.3594	0.1273	-0.0502	0.378	-0.1348	0.0046	0.66	-0.1835	-0.5507	-0.0617	0.1448	0.0464	-0.0128	0.2469	0.0307	0.2513	-17.6491	1.8147	-26.9982
3	3.6693	5.1344	0.4426	7.5039	-0.3161	3.2951	-0.2977	0.3421	-0.0174	-0.4652	0.1985	0.1114	-0.0889	-0.0791	0.0983	0.2189	-0.0159	-0.0087	0.2495	-0.0174	0.1561	-15.3355	-11.4629	-30.7322
4	1.594	0.6554	-0.3448	3.9034	-0.4342	1.1929	-0.0826	0.194	-0.0421	-0.174	0.07	-0.2159	0.1336	0.0073	0.0152	0.082	0.0086	0.0032	0.1644	-0.0001	0.1242	-8.6965	-7.5959	-21.5891
5	0.8141	0.0047	-0.6388	3.5597	0.7581	5.5739	-0.0083	0.037	0.0169	0.1141	0.0229	-0.2761	0.0109	-0.023	-0.0177	0.0995	0.0061	-0.0251	0.1601	-0.0087	0.1707	-5.7322	-3.3878	-14.2569
6	2.6162	-0.6025	0.5204	6.0621	-1.6339	1.6552	0.0431	0.0782	0.0466	0.0845	-0.0558	-0.7005	0.0592	0.3843	0.0019	0.135	-0.0094	-0.031	0.1963	-0.017	0.1906	-0.406	-2.3094	-14.0873
7	8.19	-4.2968	-5.7885	8.7401	4.9272	7.8537	0.0206	-0.322	0.3801	0.2047	0.2768	-0.308	-0.3958	0.3841	-0.331	0.2407	-0.0282	-0.0305	0.2078	-0.0025	0.2225	-4.3765	9.7594	-18.0008
8	1.269	0.1095	-0.4049	4.973	-0.4595	1.4251	-0.0971	-0.0338	-0.1769	0.194	0.0413	-0.112	0.5116	-0.0193	0.0272	0.3392	0.0183	-0.0067	0.1467	0.014	0.157	-10.58	-26.6975	-6.3914
9	1.7164	1.9379	-0.2367	9.1424	1.7354	4.1224	-0.0912	-0.0186	-0.088	0.8181	0.0903	-1.0221	0.5949	0.4091	0.0433	0.405	0.1155	-0.05	0.268	0.0275	0.3575	-3.32	-27.1633	-7.6717
10	4.8854	0.5286	0.8247	6.2382	3.2596	5.0025	0.0031	0.0491	-0.2078	0.1601	0.0555	-0.9679	-0.0682	0.3263	-0.1022	0.2123	0.0618	-0.0635	0.2624	0.0385	0.3619	3.2685	-18.8787	-12.2477
11	1.7179	-0.3541	-0.4043	3.8802	0.4354	2.9132	-0.064	0.0463	-0.0519	0.071	0.087	-0.2284	0.3244	0.0955	-0.0039	0.1687	0.0198	0.0011	0.1407	-0.0049	0.1379	-8.6253	-20.5062	-16.0858
12	6.5207	-0.3107	-0.7151	4.7797	-0.9226	2.7019	-0.0444	-0.2024	-0.2199	0.0593	0.0324	0.2824	0.3201	-0.0984	0.0265	0.1851	-0.0442	-0.0039	0.1326	-0.0125	0.0929	-17.108	-22.3164	-16.4551
13	2.2009	0.5734	0.3618	4.4717	-1.7738	4.5375	-0.0459	0.106	-0.2117	-0.1834	-0.0659	0.0372	0.6086	-0.0343	0.1231	0.2113	-0.0267	0.0321	0.1617	-0.0301	0.1542	-18.1152	-24.7091	-21.3829
14	8.8299	-3.3832	-4.6603	8.1873	5.0591	7.2262	-0.0211	0.2506	-0.5283	-0.1682	0.1984	0.2251	0.8915	-0.7213	-0.0075	0.5479	-0.0896	-0.0439	0.1907	0.0355	0.2336	-18.2727	-35.4216	-12.383

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 72 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 85 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 86 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 128 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 129 through 146 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 147 through 159 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 20 through 48 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 49 through 72 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 73 through 85 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 86 through 110 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 111 through 128 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 129 through 146 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 147 through 159 )

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