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- PDB-9t4g: Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) ... -

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Basic information

Entry
Database: PDB / ID: 9t4g
TitleHuman Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) 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 / PHOSPHATE ION / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.28 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)18,0389
Polymers17,1151
Non-polymers9238
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-83 kcal/mol
Surface area8320 Å2
Unit cell
Length a, b, c (Å)34.574, 65.682, 79.130
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: 17115.367 Da / Num. of mol.: 1
Mutation: Deletion of the last 24 C-terminal residues (149-172)
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, 270 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#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.: 262 / 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: 53.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 20 mg/mL IP6: 10 mM Precipitant condition: 28% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl and 1mM MgCl2 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: May 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.28→50.54 Å / Num. obs: 38659 / % possible obs: 91.5 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.8 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.02 / Net I/σ(I): 14.7
Reflection shellResolution: 1.28→1.37 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1933 / CC1/2: 0.8 / Rpim(I) all: 0.3

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Processing

Software
NameVersionClassification
autoPROC1.1.7data processing
REFMAC5.8.0419refinement
Coot0.9.8.92model building
REFMAC5.8.0419phasing
autoPROC1.1.7data reduction
autoPROC1.1.7data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.28→50.54 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.927 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.055 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1923 1938 5.013 %
Rwork0.1687 36721 -
all0.17 --
obs-38659 80.978 %
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: 16.934 Å2
Baniso -1Baniso -2Baniso -3
1--0.084 Å2-0 Å20 Å2
2---0.07 Å20 Å2
3---0.154 Å2
Refinement stepCycle: LAST / Resolution: 1.28→50.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 47 262 1511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121425
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161305
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.8781950
X-RAY DIFFRACTIONr_angle_other_deg0.6651.8073033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.745514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87310263
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.7751069
X-RAY DIFFRACTIONr_chiral_restr0.0990.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_nbd_refined0.2130.2227
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.21052
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2621
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.2641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1790.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2410.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2730.25
X-RAY DIFFRACTIONr_nbd_other0.2290.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2120.221
X-RAY DIFFRACTIONr_mcbond_it1.9961.538673
X-RAY DIFFRACTIONr_mcbond_other1.9951.539672
X-RAY DIFFRACTIONr_mcangle_it3.142.759864
X-RAY DIFFRACTIONr_mcangle_other3.1382.758865
X-RAY DIFFRACTIONr_scbond_it3.5222.061752
X-RAY DIFFRACTIONr_scbond_other3.5012.031725
X-RAY DIFFRACTIONr_scangle_it5.6313.61086
X-RAY DIFFRACTIONr_scangle_other5.6483.61078
X-RAY DIFFRACTIONr_lrange_it7.79320.5511614
X-RAY DIFFRACTIONr_lrange_other7.50918.1661521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.3090.417110.394169X-RAY DIFFRACTION5.1888
1.309-1.3450.351420.362633X-RAY DIFFRACTION19.8646
1.345-1.3840.383630.3261532X-RAY DIFFRACTION48.392
1.384-1.4260.331180.3122211X-RAY DIFFRACTION72.804
1.426-1.4730.2951410.2662608X-RAY DIFFRACTION88.7633
1.473-1.5250.2291390.2192795X-RAY DIFFRACTION97.2812
1.525-1.5820.2061570.2012762X-RAY DIFFRACTION99.5906
1.582-1.6470.1981530.1862662X-RAY DIFFRACTION99.8227
1.647-1.720.2341580.1662538X-RAY DIFFRACTION100
1.72-1.8040.1961210.1642463X-RAY DIFFRACTION100
1.804-1.9010.2361020.1612341X-RAY DIFFRACTION99.755
1.901-2.0160.2021170.1652227X-RAY DIFFRACTION100
2.016-2.1550.1871070.1612096X-RAY DIFFRACTION99.7284
2.155-2.3270.188880.1491961X-RAY DIFFRACTION99.7566
2.327-2.5490.1761010.1461779X-RAY DIFFRACTION99.3658
2.549-2.8490.154790.1481662X-RAY DIFFRACTION99.5995
2.849-3.2880.157830.1531446X-RAY DIFFRACTION99.6091
3.288-4.0230.17810.1331238X-RAY DIFFRACTION100
4.023-5.6710.185530.154999X-RAY DIFFRACTION99.7156
5.671-50.540.171240.249599X-RAY DIFFRACTION99.0461

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