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- PDB-9t4m: Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) ... -

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Basic information

Entry
Database: PDB / ID: 9t4m
TitleHuman Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) N112S 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: 1.78 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)17,9928
Polymers17,0881
Non-polymers9047
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-51 kcal/mol
Surface area8640 Å2
Unit cell
Length a, b, c (Å)100.131, 100.131, 34.060
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#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: 17088.342 Da / Num. of mol.: 1
Mutation: Deletion of the last 24 C-terminal residues (149-172) and N112S
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

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.9 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 24mg/mL Ip6: 10mM Precipitant condition: 31% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl, 10mM MgCl2. Ratio: 1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 13, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.78→50.07 Å / Num. obs: 19071 / % possible obs: 100 % / Redundancy: 15.9 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.13 / Net I/σ(I): 4.5
Reflection shellResolution: 1.78→1.81 Å / Mean I/σ(I) obs: 0.1 / Num. unique obs: 943 / CC1/2: 0.33 / Rpim(I) all: 6.95

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Processing

Software
NameVersionClassification
autoPROC1.1.7data processing
MOLREP11.9.02phasing
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: 1.78→50.07 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.427 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.122 / ESU R Free: 0.128
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2421 861 4.515 %
Rwork0.1867 18210 -
all0.189 --
obs-19071 99.953 %
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: 22.887 Å2
Baniso -1Baniso -2Baniso -3
1-0.183 Å20.092 Å20 Å2
2--0.183 Å2-0 Å2
3----0.594 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 48 193 1441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121402
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161248
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.8811923
X-RAY DIFFRACTIONr_angle_other_deg0.5581.7822898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8675167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.957513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78910242
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.5111067
X-RAY DIFFRACTIONr_chiral_restr0.0750.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021641
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02317
X-RAY DIFFRACTIONr_nbd_refined0.20.2256
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21149
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2598
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2661
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2152
X-RAY DIFFRACTIONr_metal_ion_refined0.0510.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.214
X-RAY DIFFRACTIONr_nbd_other0.1810.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1890.218
X-RAY DIFFRACTIONr_mcbond_it2.0712.194644
X-RAY DIFFRACTIONr_mcbond_other2.0712.195643
X-RAY DIFFRACTIONr_mcangle_it3.383.928819
X-RAY DIFFRACTIONr_mcangle_other3.3793.926820
X-RAY DIFFRACTIONr_scbond_it3.2522.753758
X-RAY DIFFRACTIONr_scbond_other3.1332.708711
X-RAY DIFFRACTIONr_scangle_it5.1964.8621104
X-RAY DIFFRACTIONr_scangle_other5.1914.8511099
X-RAY DIFFRACTIONr_lrange_it8.31226.6481580
X-RAY DIFFRACTIONr_lrange_other8.2125.5761518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.8250.31720.31317X-RAY DIFFRACTION100
1.825-1.8740.322810.2761278X-RAY DIFFRACTION100
1.874-1.9290.276680.2531253X-RAY DIFFRACTION99.9244
1.929-1.9880.258430.2271254X-RAY DIFFRACTION100
1.988-2.0530.232580.2271176X-RAY DIFFRACTION100
2.053-2.1250.22550.2041174X-RAY DIFFRACTION100
2.125-2.2050.181540.1751103X-RAY DIFFRACTION100
2.205-2.2950.214530.1781061X-RAY DIFFRACTION100
2.295-2.3970.218420.1641026X-RAY DIFFRACTION100
2.397-2.5130.244620.165981X-RAY DIFFRACTION100
2.513-2.6490.239470.171946X-RAY DIFFRACTION100
2.649-2.8090.217300.179901X-RAY DIFFRACTION100
2.809-3.0030.26470.169821X-RAY DIFFRACTION100
3.003-3.2420.235380.174782X-RAY DIFFRACTION100
3.242-3.550.282330.185728X-RAY DIFFRACTION100
3.55-3.9670.189150.173667X-RAY DIFFRACTION100
3.967-4.5750.204140.14608X-RAY DIFFRACTION100
4.575-5.5920.212210.134505X-RAY DIFFRACTION100
5.592-7.860.281170.202391X-RAY DIFFRACTION100
7.86-50.070.288110.226238X-RAY DIFFRACTION100

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