3MCF | pdb_00003mcf

Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 3-alpha

• PDB DOI: https://doi.org/10.2210/pdb3MCF/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-03-29 Released: 2010-04-07 
• Deposition Author(s): Tresaugues, L., Welin, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., van der Berg, S., Wahlberg, E., Weigelt, J., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.217 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human diphosphoinositol polyphosphate phosphohydrolase 3-alpha

Tresaugues, L., Welin, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., van der Berg, S., Wahlberg, E., Weigelt, J., Wisniewska, M., Nordlund, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.05 kDa 
• Atom Count: 2,321 
• Modeled Residue Count: 253 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diphosphoinositol polyphosphate phosphohydrolase 3-alpha	A, B	136	Homo sapiens	Mutation(s): 1  Gene Names: APS2, DIPP3A, NUDT10 EC: 3.6.1.52 (PDB Primary Data), 3.6.1 (PDB Primary Data), 3.6.1.60 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NFP7 (Homo sapiens) Explore Q8NFP7  Go to UniProtKB:  Q8NFP7
PHAROS:  Q8NFP7 GTEx:  ENSG00000122824

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth A], D [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.217 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.39	α = 90
b = 79.549	β = 90
c = 88.729	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Tresaugues, L., Welin, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kol, S., Kotenyova, T., Moche, M., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Thorsell, A.G., van der Berg, S., Wahlberg, E., Weigelt, J., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-06
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description