2FVV | pdb_00002fvv

Human Diphosphoinositol polyphosphate phosphohydrolase 1

• PDB DOI: https://doi.org/10.2210/pdb2FVV/pdb

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


• Deposited: 2006-01-31 Released: 2006-03-11 
• Deposition Author(s): Hallberg, B.M., Kursula, P., Ogg, D., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Graslund, S., Hammarstrom, M., Hogbom, M., Holmberg-Schiavone, L., Kotenyova, T., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., van den Berg, S., Weigelt, J., Persson, C., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.222 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.171 (Depositor) 

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 
• DOI: https://doi.org/10.1002/prot.22489
• Primary Citation Related Structures: 
  2FVV, 2Q9P

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.85 kDa 
• Atom Count: 1,415 
• Modeled Residue Count: 135 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

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 (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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHP	D [auth A]	INOSITOL HEXAKISPHOSPHATE C6 H18 O24 P6 IMQLKJBTEOYOSI-GPIVLXJGSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.222 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.653	α = 90
b = 59.9	β = 90
c = 61.735	γ = 90

Software Package:

Software Name	Purpose
SHELX	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
SAINT	data reduction
XDS	data reduction
SADABS	data scaling
XSCALE	data scaling
SHELXD	phasing
SHELXL-97	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-11 
Deposition Author(s): Hallberg, B.M., Kursula, P., Ogg, D., Arrowsmith, C., Berglund, H., Edwards, A., Ehn, M., Flodin, S., Graslund, S., Hammarstrom, M., Hogbom, M., Holmberg-Schiavone, L., Kotenyova, T., Nilsson-Ehle, P., Nordlund, P., Nyman, T., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., van den Berg, S., Weigelt, J., Persson, C., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2006-03-11
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-05-23
  Changes: Data collection
• Version 2.0: 2019-04-03
  Changes: Advisory, Atomic model, Data collection
• Version 2.1: 2020-10-14
  Changes: Database references, Derived calculations, Structure summary
• Version 2.2: 2024-03-13
  Changes: Data collection, Database references