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- PDB-9da4: Crystal structure of human DNPH1 bound to inhibitor 2b -

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Basic information

Entry
Database: PDB / ID: 9da4
TitleCrystal structure of human DNPH1 bound to inhibitor 2b
Components5-hydroxymethyl-dUMP N-hydrolase
KeywordsHYDROLASE/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 ...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 / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
2-deoxynucleoside 5-phosphate N-hydrolase 1, DNPH1 / : / Nucleoside 2-deoxyribosyltransferase / Nucleoside 2-deoxyribosyltransferase
Similarity search - Domain/homology
: / 5-hydroxymethyl-dUMP N-hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsWagner, A.G. / Schramm, V.L. / Almo, S.C. / Ghosh, A.
Funding support United States, 2items
OrganizationGrant numberCountry
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
CitationJournal: 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
DepositionAug 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-hydroxymethyl-dUMP N-hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5682
Polymers16,2241
Non-polymers3431
Water1,40578
1
A: 5-hydroxymethyl-dUMP N-hydrolase
hetero molecules

A: 5-hydroxymethyl-dUMP N-hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1354
Polymers32,4482
Non-polymers6872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area3180 Å2
ΔGint-32 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.304, 83.304, 80.587
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

21A-375-

HOH

31A-376-

HOH

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Components

#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.: 1
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-A1BBE / {(3R,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-hydroxypyrrolidin-3-yl}methyl dihydrogen phosphate


Mass: 343.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N5O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% (w/v) PEG 3350, 0.2 M Ammonium acetate and 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.73→27.27 Å / Num. obs: 17730 / % possible obs: 100 % / Redundancy: 21.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.022 / Rrim(I) all: 0.104 / Χ2: 1 / Net I/σ(I): 19.1 / Num. measured all: 388195
Reflection shellResolution: 1.73→1.77 Å / % possible obs: 99.7 % / Redundancy: 20.2 % / Rmerge(I) obs: 0.828 / Num. measured all: 19254 / Num. unique obs: 951 / CC1/2: 0.938 / Rpim(I) all: 0.186 / Rrim(I) all: 0.849 / Χ2: 0.98 / Net I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→27.27 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 853 4.82 %
Rwork0.184 --
obs0.1863 17684 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→27.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 23 78 1222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.956
X-RAY DIFFRACTIONf_dihedral_angle_d5.834167
X-RAY DIFFRACTIONf_chiral_restr0.058167
X-RAY DIFFRACTIONf_plane_restr0.011206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.840.24851300.19092740X-RAY DIFFRACTION100
1.84-1.980.24941490.20282745X-RAY DIFFRACTION100
1.98-2.180.26021150.19652784X-RAY DIFFRACTION100
2.18-2.50.23181280.1892779X-RAY DIFFRACTION100
2.5-3.150.24991670.20312802X-RAY DIFFRACTION100
3.15-27.270.21021640.16882981X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.6466-0.98070.29322.02750.09892.25650.04090.10970.0446-0.0830.0494-0.1665-0.0856-0.0209-0.05490.2765-0.07040.01770.331-0.01520.2434-19.1734.2146-8.5775
22.23060.08930.13873.30680.51744.07350.0055-0.1236-0.2250.1990.0994-0.30730.45760.1986-0.1030.2077-0.0294-0.02410.24310.00210.2428-14.666428.20788.2295
37.68660.4097-0.39886.62241.51279.06460.25830.1431-0.59190.60480.1365-1.14021.33671.4764-0.33490.5350.1521-0.04340.5018-0.01720.5106-5.678817.59093.805
42.07841.76321.01552.1111-0.18742.0598-0.24480.3704-0.2351-0.41860.4441-0.65350.01760.3346-0.20050.2297-0.07920.05870.2903-0.06230.2991-13.657929.0399-3.6051
54.11642.3010.20527.42432.31514.05620.11290.4216-0.1779-0.62740.3469-1.20760.03670.7175-0.35330.26720.01520.06940.4336-0.10420.3974-5.620424.9971-4.5524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 86 )
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 146 )
3X-RAY DIFFRACTION3chain 'A' and (resid 147 through 159 )
4X-RAY DIFFRACTION4chain 'A' and (resid 18 through 35 )
5X-RAY DIFFRACTION5chain 'A' and (resid 36 through 48 )

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