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- PDB-9t49: Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) ... -

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Basic information

Entry
Database: PDB / ID: 9t49
TitleHuman Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) in complex with 1,5-(PCP)-IP5 (PCP-IP8)
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / Inositol metabolism / phosphatase / NUDIX hydrolases / DIPP1 / IP8
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
Chem-4WZ / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)18,1008
Polymers17,1151
Non-polymers9847
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-52 kcal/mol
Surface area8320 Å2
Unit cell
Length a, b, c (Å)99.149, 99.149, 34.154
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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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: 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
#2: Chemical ChemComp-4WZ / {[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid)


Mass: 816.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H24O28P8 / 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.: 205 / 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: 2.9 Å3/Da / Density % sol: 57.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 20.4 PCP-IP8: 5mM Precipitant condition: 27% 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: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.5→49.57 Å / Num. obs: 29778 / % possible obs: 96.7 % / Redundancy: 20.8 % / Biso Wilson estimate: 15 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.04 / Net I/σ(I): 15.3
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1454 / CC1/2: 0.8 / Rpim(I) all: 0.4

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Processing

Software
NameVersionClassification
autoPROC1.0.5data processing
MOLREP11.9.02phasing
REFMAC5.8.0419refinement
Coot0.9.8.92model building
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.57 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.101 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1792 1560 5.239 %
Rwork0.1531 28218 -
all0.154 --
obs-29778 96.704 %
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: 17.614 Å2
Baniso -1Baniso -2Baniso -3
1-0.253 Å20.127 Å20 Å2
2--0.253 Å2-0 Å2
3----0.822 Å2
Refinement stepCycle: LAST / Resolution: 1.5→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 50 205 1426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121299
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161186
X-RAY DIFFRACTIONr_angle_refined_deg2.1441.8861770
X-RAY DIFFRACTIONr_angle_other_deg0.7071.7912747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6595154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.283513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05910232
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.851063
X-RAY DIFFRACTIONr_chiral_restr0.1090.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021530
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02300
X-RAY DIFFRACTIONr_nbd_refined0.2180.2224
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.21040
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2585
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2662
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2153
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.215
X-RAY DIFFRACTIONr_nbd_other0.2460.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2530.217
X-RAY DIFFRACTIONr_mcbond_it2.151.524607
X-RAY DIFFRACTIONr_mcbond_other2.1521.523606
X-RAY DIFFRACTIONr_mcangle_it3.272.709764
X-RAY DIFFRACTIONr_mcangle_other3.2672.708765
X-RAY DIFFRACTIONr_scbond_it4.1692.157692
X-RAY DIFFRACTIONr_scbond_other4.1722.159690
X-RAY DIFFRACTIONr_scangle_it6.6313.7281006
X-RAY DIFFRACTIONr_scangle_other6.6283.7271007
X-RAY DIFFRACTIONr_lrange_it9.04422.2211500
X-RAY DIFFRACTIONr_lrange_other8.80820.1841434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5440.2621200.2552048X-RAY DIFFRACTION95.5908
1.544-1.5860.2131150.2151950X-RAY DIFFRACTION94.8118
1.586-1.6320.2391020.191957X-RAY DIFFRACTION95.9013
1.632-1.6820.197940.1781894X-RAY DIFFRACTION95.3935
1.682-1.7370.2221000.171842X-RAY DIFFRACTION96.8096
1.737-1.7980.18920.1561777X-RAY DIFFRACTION95.0661
1.798-1.8660.1811020.1551717X-RAY DIFFRACTION97.3248
1.866-1.9420.184870.1491706X-RAY DIFFRACTION97.658
1.942-2.0280.205990.1531552X-RAY DIFFRACTION95.8212
2.028-2.1270.163900.1411541X-RAY DIFFRACTION97.0833
2.127-2.2420.127900.1381462X-RAY DIFFRACTION98.1657
2.242-2.3770.182640.1381426X-RAY DIFFRACTION98.2202
2.377-2.5410.177610.1371310X-RAY DIFFRACTION97.6496
2.541-2.7440.17780.1311223X-RAY DIFFRACTION98.1146
2.744-3.0050.168540.1351153X-RAY DIFFRACTION98.4502
3.005-3.3580.155560.141040X-RAY DIFFRACTION98.917
3.358-3.8750.117350.131858X-RAY DIFFRACTION91.0296
3.875-4.7380.144540.125788X-RAY DIFFRACTION99.645
4.738-6.670.22440.204609X-RAY DIFFRACTION99.2401
6.67-49.570.284230.235365X-RAY DIFFRACTION99.7429

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