PDB-9t48: Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) ...

ID or keywords:

Entry

Database: PDB / ID: 9t48

Title

Human Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1) R89S mutant in complex with 1,5-(PCP)-IP5 (PCP-IP8)

Components

Diphosphoinositol polyphosphate phosphohydrolase 1

Keywords

HYDROLASE / Inositol metabolism / phosphatase / NUDIX hydrolases / DIPP1 / IP8 / twist-boat / for 1-PP hydrolysis

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Casas-Florez, D. / Marquez-Monino, M.A. / Gonzalez, B.

Funding support

Spain, 2items

Citation

Journal: 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

Deposition	Oct 30, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 10, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9t48.cif.gz	56.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9t48.ent.gz	37.1 KB	Display	PDB format
PDBx/mmJSON format	9t48.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t4/9t48 ftp://data.pdbj.org/pub/pdb/validation_reports/t4/9t48	HTTPS FTP

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Related structure data

Related structure data	9t49C 9t4aC 9t4bC 9t4cC 9t4dC 9t4eC 9t4fC 9t4gC 9t4hC 9t4iC 9t4jC 9t4kC 9t4lC 9t4mC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (7) #86 - Feb 2007 Exosomes similarity (1) #201 - Sep 2016 Isoprene Synthase similarity (4)

Deposited unit

A: Diphosphoinositol polyphosphate phosphohydrolase 1

hetero molecules

18 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	34.272, 65.070, 78.416
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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
#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.: 3 / 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.: 187 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 53.2 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Protein: 20mg/mL PCP-IP8: 10mM Precipitant condition: 20% PEG 6K, 0.1M NaOAc pH 5, 0.2M LiCl,10mM MgCl2 Ratio: 1:1

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 1.5→78.42 Å / Num. obs: 28885 / % possible obs: 100 % / Redundancy: 12.2 % / B_iso Wilson estimate: 19.6 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.03 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1376 / CC_1/2: 0.521 / R_pim(I) all: 0.661

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Processing

Software

Name	Version	Classification
autoPROC	1.0.5	data reduction
Aimless	0.7.13	data scaling
MOLREP	11.9.02	phasing
REFMAC	5.8.0431	refinement
Coot	0.9.8.92	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→50.075 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.96 / SU B: 1.788 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1954	1444	5.01 %	RANDOM
R_work	0.1758	27381	-	-
all	0.177	-	-	-
obs	-	28825	99.965 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23.516 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.628 Å²	0 Å²	-0 Å²
2-	-	-1.089 Å²	0 Å²
3-	-	-	2.717 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→50.075 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1141	0	49	187	1377

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	1341
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1175
X-RAY DIFFRACTION	r_angle_refined_deg	1.912	1.889	1854
X-RAY DIFFRACTION	r_angle_other_deg	0.651	1.784	2727
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.857	5	158
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.586	5	13
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.363	10	222
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.476	10	65
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	205
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1566
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	308
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	226
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	1049
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	593
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	653
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.237	0.2	132
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.113	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.248	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.338	0.2	3
X-RAY DIFFRACTION	r_nbd_other	0.194	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.135	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	2.112	2.156	608
X-RAY DIFFRACTION	r_mcbond_other	2.111	2.156	608
X-RAY DIFFRACTION	r_mcangle_it	3.033	3.868	774
X-RAY DIFFRACTION	r_mcangle_other	3.031	3.868	775
X-RAY DIFFRACTION	r_scbond_it	3.736	2.951	733
X-RAY DIFFRACTION	r_scbond_other	3.745	2.951	728
X-RAY DIFFRACTION	r_scangle_it	6.13	5.329	1080
X-RAY DIFFRACTION	r_scangle_other	6.127	5.327	1081
X-RAY DIFFRACTION	r_lrange_it	7.657	24.855	1472
X-RAY DIFFRACTION	r_lrange_other	7.459	23.823	1423

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.5-1.539	0.285	107	0.313	1975	0.311	2084	0.861	0.853	99.904	0.291
1.539-1.581	0.296	102	0.287	1937	0.287	2042	0.876	0.889	99.8531	0.26
1.581-1.627	0.253	91	0.255	1916	0.255	2007	0.919	0.924	100	0.224
1.627-1.677	0.274	101	0.236	1805	0.238	1906	0.942	0.945	100	0.207
1.677-1.732	0.266	91	0.224	1791	0.226	1883	0.949	0.953	99.9469	0.193
1.732-1.793	0.237	92	0.199	1738	0.201	1830	0.957	0.964	100	0.171
1.793-1.86	0.219	85	0.185	1655	0.187	1740	0.965	0.972	100	0.16
1.86-1.936	0.217	70	0.166	1623	0.168	1693	0.969	0.979	100	0.144
1.936-2.022	0.195	78	0.153	1562	0.155	1640	0.976	0.983	100	0.138
2.022-2.12	0.186	72	0.152	1475	0.153	1547	0.979	0.984	100	0.136
2.12-2.235	0.168	90	0.149	1406	0.15	1496	0.979	0.985	100	0.136
2.235-2.37	0.156	80	0.14	1334	0.141	1414	0.979	0.987	100	0.131
2.37-2.533	0.132	68	0.146	1258	0.145	1326	0.988	0.986	100	0.137
2.533-2.736	0.201	60	0.16	1182	0.162	1242	0.969	0.982	100	0.154
2.736-2.996	0.152	65	0.164	1090	0.163	1156	0.98	0.982	99.9135	0.159
2.996-3.348	0.189	53	0.166	997	0.167	1050	0.973	0.982	100	0.168
3.348-3.863	0.17	46	0.157	895	0.157	942	0.984	0.984	99.8938	0.162
3.863-4.724	0.179	45	0.149	759	0.15	804	0.979	0.985	100	0.159
4.724-6.652	0.198	28	0.201	613	0.201	642	0.98	0.979	99.8442	0.219
6.652-50.075	0.323	20	0.247	370	0.25	391	0.948	0.952	99.7442	0.264

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