4ZKF | pdb_00004zkf

Crystal structure of human phosphodiesterase 12

• PDB DOI: https://doi.org/10.2210/pdb4ZKF/pdb

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


• Deposited: 2015-04-30 Released: 2015-06-17 
• Deposition Author(s): Kim, S.Y., Kohno, T., Mori, T., Kitano, K., Hakoshima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Crystal structure of human phosphodiesterase

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

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)

Macromolecule Content 

• Total Structure Weight: 51.95 kDa 
• Atom Count: 4,121 
• Modeled Residue Count: 462 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2',5'-phosphodiesterase 12	A	462	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.817	α = 90
b = 99.84	β = 90
c = 104.69	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-06-17 
Deposition Author(s): Kim, S.Y., Kohno, T., Mori, T., Kitano, K., Hakoshima, T.

Revision History  

• 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
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations