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- PDB-9t4l: HumanDiphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) E... -

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Basic information

Entry
Database: PDB / ID: 9t4l
TitleHumanDiphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) E108N mutant in complex with IP6
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / Inositol metabolism / phosphatase / NUDIX hydrolases / DIPP1 / IP6
Function / homology
Function and homology information


inositol diphosphate pentakisphosphate diphosphatase activity / diphosphoinositol polyphosphate catabolic process / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / bis(5'-adenosyl)-hexaphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process ...inositol diphosphate pentakisphosphate diphosphatase activity / diphosphoinositol polyphosphate catabolic process / inositol diphosphate tetrakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / bis(5'-adenosyl)-hexaphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / endopolyphosphatase activity / diphosphoinositol polyphosphate metabolic process / diphosphoinositol-polyphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / diadenosine hexaphosphate hydrolase (ATP-forming) / bis(5'-adenosyl)-pentaphosphatase activity / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-polyphosphate diphosphatase / RNA decapping / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / manganese ion binding / cell-cell signaling / glutamatergic synapse / magnesium ion binding / zinc ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.13 Å
AuthorsCasas-Florez, D. / Marquez-Monino, M.A. / Gonzalez, B.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-117400GB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2023-147659NB-I00 Spain
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: The DIPP1 family binds IP 8 in catalytically-productive twist-boat and chair conformations and associates in a ligand-dependent manner.
Authors: Casas-Florez, D. / Whitfield, H. / Perez-Canadillas, J.M. / Monterroso, B. / Riley, A.M. / Marquez-Monino, M.A. / Shipton, M.L. / Sanz-Aparicio, J. / Brearley, C.A. / Potter, B.V.L. / Gonzalez, B.
History
DepositionOct 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diphosphoinositol polyphosphate phosphohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2558
Polymers17,4271
Non-polymers8287
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-77 kcal/mol
Surface area8540 Å2
Unit cell
Length a, b, c (Å)34.473, 65.398, 77.972
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diphosphoinositol polyphosphate phosphohydrolase 1 / DIPP-1 / Diadenosine hexaphosphate hydrolase / Ap6A hydrolase / Endopolyphosphatase / Nucleoside ...DIPP-1 / Diadenosine hexaphosphate hydrolase / Ap6A hydrolase / Endopolyphosphatase / Nucleoside diphosphate-linked moiety X motif 3 / Nudix motif 3 / m7GpppN-mRNA hydrolase / m7GpppX diphosphatase


Mass: 17426.752 Da / Num. of mol.: 1
Mutation: Deletion of the last 24 C-terminal residues (149-172) and E108N
Source method: isolated from a genetically manipulated source
Details: Deletion of the last 24 C-terminal residues (149-172), the first three amino acids (GHM) remain as residual residues after removal of the expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT3, DIPP, DIPP1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Star
References: UniProt: O95989, diphosphoinositol-polyphosphate diphosphatase, diadenosine hexaphosphate hydrolase (ATP-forming), endopolyphosphatase, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] ...References: UniProt: O95989, diphosphoinositol-polyphosphate diphosphatase, diadenosine hexaphosphate hydrolase (ATP-forming), endopolyphosphatase, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase, 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.6 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 20mg/mL IP6: 10mM Precipitant condition: 25% PEG 3350, 0.1M Bis-Tris pH 5.5, 0.2M NaCl Ratio: 1:2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.13→50.1 Å / Num. obs: 51069 / % possible obs: 94.4 % / Redundancy: 11.8 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02 / Net I/σ(I): 16.72
Reflection shellResolution: 1.13→1.23 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2523 / CC1/2: 0.67 / Rpim(I) all: 0.38

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
REFMAC5.8.0419refinement
Coot0.9.8.92model building
autoPROC1.1.7data reduction
autoPROC1.1.7data scaling
REFMAC5.8.0419phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.13→50.1 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 0.698 / SU ML: 0.031 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.047
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2035 2564 5.021 %
Rwork0.1731 48505 -
all0.175 --
obs-51069 76.255 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.848 Å2
Baniso -1Baniso -2Baniso -3
1-0.062 Å20 Å2-0 Å2
2---0.076 Å20 Å2
3---0.014 Å2
Refinement stepCycle: LAST / Resolution: 1.13→50.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 42 239 1490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121399
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161263
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.8881917
X-RAY DIFFRACTIONr_angle_other_deg0.71.7942930
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.583513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56910249
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.4671067
X-RAY DIFFRACTIONr_chiral_restr0.110.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021628
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02318
X-RAY DIFFRACTIONr_nbd_refined0.2170.2228
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21082
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2594
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2655
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2180
X-RAY DIFFRACTIONr_metal_ion_refined0.4240.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2090.28
X-RAY DIFFRACTIONr_nbd_other0.1760.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.218
X-RAY DIFFRACTIONr_mcbond_it1.6331.429642
X-RAY DIFFRACTIONr_mcbond_other1.6261.429642
X-RAY DIFFRACTIONr_mcangle_it2.4282.563813
X-RAY DIFFRACTIONr_mcangle_other2.4262.562814
X-RAY DIFFRACTIONr_scbond_it3.2111.882757
X-RAY DIFFRACTIONr_scbond_other3.2551.887710
X-RAY DIFFRACTIONr_scangle_it4.9313.2681104
X-RAY DIFFRACTIONr_scangle_other4.9423.2651099
X-RAY DIFFRACTIONr_lrange_it7.2419.231557
X-RAY DIFFRACTIONr_lrange_other7.02617.4551471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.1590.52970.388155X-RAY DIFFRACTION3.3136
1.159-1.190.296380.315777X-RAY DIFFRACTION17.0288
1.19-1.2250.312840.31335X-RAY DIFFRACTION30.9353
1.225-1.2630.359990.2812215X-RAY DIFFRACTION51.2855
1.263-1.3040.2931570.262826X-RAY DIFFRACTION68.2765
1.304-1.350.2961690.2473644X-RAY DIFFRACTION90.1632
1.35-1.4010.2432070.2163865X-RAY DIFFRACTION99.7795
1.401-1.4580.2512170.2013731X-RAY DIFFRACTION100
1.458-1.5230.2131650.183629X-RAY DIFFRACTION99.9473
1.523-1.5970.1842030.1743425X-RAY DIFFRACTION100
1.597-1.6830.2061710.1663279X-RAY DIFFRACTION100
1.683-1.7850.1811610.1663105X-RAY DIFFRACTION100
1.785-1.9080.1741550.1572944X-RAY DIFFRACTION100
1.908-2.0610.1661580.1572719X-RAY DIFFRACTION100
2.061-2.2570.1671170.1522563X-RAY DIFFRACTION100
2.257-2.5230.1691330.152282X-RAY DIFFRACTION100
2.523-2.9120.1891160.1572042X-RAY DIFFRACTION100
2.912-3.5630.204960.1631749X-RAY DIFFRACTION100
3.563-5.0270.215580.1441409X-RAY DIFFRACTION100
5.027-50.10.266530.263811X-RAY DIFFRACTION99.8844

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