2Q9P | pdb_00002q9p

Human diphosphoinositol polyphosphate phosphohydrolase 1, Mg-F complex

PDB DOI: https://doi.org/10.2210/pdb2Q9P/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-06-13 Released: 2007-09-11
Deposition Author(s): Thorsell, A.G., Busam, R., Arrowsmith, C.H., Berglund, H., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Holmberg-Schiavone, L., Johansson, I., Kallas, A., Karlberg, T., Kotenyova, T., Lehtio, L., Moche, M., Nordlund, P., Nyman, T., Ogg, D., Sagemark, J., Sundstrom, M., Van den Berg, S., Weigelt, J., Welin, M., Persson, C., Hallberg, B.M., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.230 (Depositor), 0.234 (DCC)
R-Value Work:
0.192 (Depositor), 0.197 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of human diphosphoinositol phosphatase 1.

Thorsell, A.G., Persson, C., Graslund, S., Hammarstrom, M., Busam, R.D., Hallberg, B.M.

(2009) Proteins 77: 242-246

PubMed: 19585659 Search on PubMed
DOI: https://doi.org/10.1002/prot.22489
Primary Citation Related Structures:
2FVV, 2Q9P

Organizational Affiliation

Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden.

Macromolecule Content

Total Structure Weight: 23.04 kDa
Atom Count: 1,343
Modeled Residue Count: 132
Deposited Residue Count: 194
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diphosphoinositol polyphosphate phosphohydrolase 1	A	194	Homo sapiens	Mutation(s): 0 Gene Names: NUDT3, DIPP, DIPP1 EC: 3.6.1.52 (PDB Primary Data), 3.6.1.62 (UniProt), 3.6.1.61 (UniProt), 3.6.1.59 (UniProt), 3.6.1.10 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95989 (Homo sapiens) Explore O95989 Go to UniProtKB: O95989
PHAROS: O95989 GTEx: ENSG00000272325
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O95989
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IHP Query on IHP Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	B [auth A], C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
F Query on F Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	FLUORIDE ION F KRHYYFGTRYWZRS-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.230 (Depositor), 0.234 (DCC)
R-Value Work: 0.192 (Depositor), 0.197 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.193	α = 90
b = 59.444	β = 90
c = 62.547	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
SAINT	data reduction
SADABS	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Holmberg-Schiavone, L.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-09-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-10-14
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-08-30
Changes: Data collection, Database references, Refinement description