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- PDB-9t4j: Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) ... -

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Basic information

Entry
Database: PDB / ID: 9t4j
TitleHuman Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) H91E 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 / SULFITE ION / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.324 Å
AuthorsCasas-Florez, D. / Marquez-Monino, M.A. / Gonzalez, B.
Funding support Spain, 3items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2020-117400GB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2023-147659NB-I00 Spain
Ministerio de Ciencia e Innovacion (MCIN)PID2020-117400GB-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

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Assembly

Deposited unit
A: Diphosphoinositol polyphosphate phosphohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0909
Polymers17,1061
Non-polymers9848
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-46 kcal/mol
Surface area8100 Å2
Unit cell
Length a, b, c (Å)34.031, 65.106, 79.234
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: 17106.334 Da / Num. of mol.: 1
Mutation: Deletion of the last 24 C-terminal residues (149-172) and H91E
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 , 6 types, 191 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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 condition: 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: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.324→79.23 Å / Num. obs: 41338 / % possible obs: 98.7 % / Redundancy: 12.1 % / Biso Wilson estimate: 17.2 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.02 / Net I/σ(I): 19.1
Reflection shellResolution: 1.324→1.35 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1966 / CC1/2: 0.85 / Rpim(I) all: 0.265

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
Aimless0.7.13data scaling
REFMAC5.8.0419refinement
Coot0.9.8.92model building
REFMAC5.8.0419phasing
autoPROC1.0.5data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.324→50.303 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.945 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.054 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2056 2087 5.057 %
Rwork0.1763 39182 -
all0.178 --
obs-41269 98.654 %
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: 20.096 Å2
Baniso -1Baniso -2Baniso -3
1--1.112 Å2-0 Å20 Å2
2---0.479 Å20 Å2
3---1.591 Å2
Refinement stepCycle: LAST / Resolution: 1.324→50.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 52 183 1421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121503
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161351
X-RAY DIFFRACTIONr_angle_refined_deg2.2661.8942068
X-RAY DIFFRACTIONr_angle_other_deg0.7711.8053145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7945184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.577515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07510266
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.1831072
X-RAY DIFFRACTIONr_chiral_restr0.1140.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021795
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02343
X-RAY DIFFRACTIONr_nbd_refined0.2160.2275
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21187
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2600
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2155
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0480.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1650.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3590.214
X-RAY DIFFRACTIONr_nbd_other0.2650.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2360.226
X-RAY DIFFRACTIONr_mcbond_it2.1251.757691
X-RAY DIFFRACTIONr_mcbond_other2.121.757690
X-RAY DIFFRACTIONr_mcangle_it3.1223.124890
X-RAY DIFFRACTIONr_mcangle_other3.123.123891
X-RAY DIFFRACTIONr_scbond_it3.9082.547812
X-RAY DIFFRACTIONr_scbond_other3.9052.551813
X-RAY DIFFRACTIONr_scangle_it5.734.5751178
X-RAY DIFFRACTIONr_scangle_other5.7274.5791179
X-RAY DIFFRACTIONr_lrange_it8.84826.9641660
X-RAY DIFFRACTIONr_lrange_other8.8426.9631660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.324-1.3580.3321500.2728220.27330640.9430.94596.99740.241
1.358-1.3960.2551370.24627990.24729360.9590.9551000.216
1.396-1.4360.2611620.22427280.22628900.9620.9651000.191
1.436-1.480.2521400.21227010.21428410.9550.9691000.178
1.48-1.5290.211390.1925580.19126970.9690.9741000.161
1.529-1.5820.2191240.18425120.18526360.9710.9761000.154
1.582-1.6420.1891210.17924370.1825580.9740.9791000.154
1.642-1.7090.1911150.17523600.17624750.9720.9791000.154
1.709-1.7850.2041350.18622120.18723470.9750.9761000.165
1.785-1.8720.198990.17421680.17522680.9770.9899.95590.161
1.872-1.9730.1951050.16515900.16721590.9740.98278.50860.159
1.973-2.0920.208950.16519570.16720520.9750.9841000.164
2.092-2.2370.201980.16718380.16919360.9750.9841000.171
2.237-2.4150.211750.16117170.16317950.9770.98599.83290.17
2.415-2.6450.2031050.15815640.16116690.9740.9841000.174
2.645-2.9560.178810.16714320.16715130.9790.9821000.187
2.956-3.4120.209670.16612990.16813670.9680.98299.92680.196
3.412-4.1740.182610.1510920.15211530.9780.9861000.187
4.174-5.8830.205480.1778690.1789190.9830.98399.78240.227
5.883-50.3030.235300.2545260.2535560.980.9621000.341

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