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- PDB-9t4i: Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) ... -

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Basic information

Entry
Database: PDB / ID: 9t4i
TitleHuman Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R89S 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: 1.408 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)17,9257
Polymers17,0451
Non-polymers8796
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-41 kcal/mol
Surface area8400 Å2
Unit cell
Length a, b, c (Å)34.288, 65.483, 78.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 17045.250 Da / Num. of mol.: 1
Mutation: Deletion of the last 24 C-terminal residues (149-172) and R89S
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, 221 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 24.305 Da / Num. of mol.: 1 / 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.: 215 / 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: 2.6 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 20mg/mL IP6: 5mM Precipitant conditions: 26% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl Ratio: 1:1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.4→39.47 Å / Num. obs: 28543 / % possible obs: 94.1 % / Redundancy: 12.6 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.04 / Net I/σ(I): 11.1
Reflection shellResolution: 1.4→1.51 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1427 / CC1/2: 0.673 / Rpim(I) all: 0.483

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Processing

Software
NameVersionClassification
autoPROC1.1.7data 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: 1.408→39.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.349 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2113 1379 4.832 %
Rwork0.1695 27162 -
all0.172 --
obs-28541 80.997 %
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: 16.493 Å2
Baniso -1Baniso -2Baniso -3
1--0.132 Å2-0 Å20 Å2
2--0.109 Å2-0 Å2
3---0.023 Å2
Refinement stepCycle: LAST / Resolution: 1.408→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 47 215 1436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121380
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161226
X-RAY DIFFRACTIONr_angle_refined_deg1.91.8821896
X-RAY DIFFRACTIONr_angle_other_deg0.6511.7752847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.851512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34910235
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.9971066
X-RAY DIFFRACTIONr_chiral_restr0.0910.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021611
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02311
X-RAY DIFFRACTIONr_nbd_refined0.2050.2213
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.21036
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2587
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2155
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0080.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2740.28
X-RAY DIFFRACTIONr_nbd_other0.2380.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2420.223
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0370.21
X-RAY DIFFRACTIONr_mcbond_it1.8961.434632
X-RAY DIFFRACTIONr_mcbond_other1.8971.434631
X-RAY DIFFRACTIONr_mcangle_it2.9762.56804
X-RAY DIFFRACTIONr_mcangle_other2.9742.559805
X-RAY DIFFRACTIONr_scbond_it3.1192.025748
X-RAY DIFFRACTIONr_scbond_other3.1182.028749
X-RAY DIFFRACTIONr_scangle_it4.8533.551092
X-RAY DIFFRACTIONr_scangle_other4.8513.5531093
X-RAY DIFFRACTIONr_lrange_it7.25920.6991519
X-RAY DIFFRACTIONr_lrange_other6.97218.3051447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.408-1.4450.24360.28895X-RAY DIFFRACTION3.9438
1.445-1.4840.332260.275491X-RAY DIFFRACTION20.5322
1.484-1.5270.299630.2771168X-RAY DIFFRACTION51.2703
1.527-1.5740.25810.2421641X-RAY DIFFRACTION72.4443
1.574-1.6250.279880.241903X-RAY DIFFRACTION86.9432
1.625-1.6820.254970.2222028X-RAY DIFFRACTION95.5915
1.682-1.7460.2491070.2062025X-RAY DIFFRACTION99.8127
1.746-1.8170.246860.1951995X-RAY DIFFRACTION100
1.817-1.8980.251970.1671902X-RAY DIFFRACTION99.95
1.898-1.990.194890.1571792X-RAY DIFFRACTION99.9469
1.99-2.0970.19860.1541739X-RAY DIFFRACTION100
2.097-2.2240.19940.1421612X-RAY DIFFRACTION99.9414
2.224-2.3770.18850.1441562X-RAY DIFFRACTION100
2.377-2.5670.207720.1551439X-RAY DIFFRACTION100
2.567-2.8110.208770.1521336X-RAY DIFFRACTION100
2.811-3.140.179510.1581226X-RAY DIFFRACTION100
3.14-3.6220.189530.1471093X-RAY DIFFRACTION100
3.622-4.4270.156600.136915X-RAY DIFFRACTION99.8975
4.427-6.2220.255410.174743X-RAY DIFFRACTION100
6.222-39.470.334200.26457X-RAY DIFFRACTION99.1684

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