4ZKF

Crystal structure of human phosphodiesterase 12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of human phosphodiesterase

Kim, S.Y.Kohno, T.Mori, T.Kitano, K.Hakoshima, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
2',5'-phosphodiesterase 12A462Homo sapiensMutation(s): 0 
Gene Names: PDE12
EC: 3.1.4 (PDB Primary Data), 3.1.13.4 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q6L8Q7 (Homo sapiens)
Explore Q6L8Q7 
Go to UniProtKB:  Q6L8Q7
PHAROS:  Q6L8Q7
GTEx:  ENSG00000174840 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6L8Q7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.817α = 90
b = 99.84β = 90
c = 104.69γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Structure summary
  • Version 1.2: 2020-02-19
    Changes: Data collection, Derived calculations, Source and taxonomy