5JO3 | pdb_00005jo3

PDE5A for NaV1.7

• PDB DOI: https://doi.org/10.2210/pdb5JO3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2016-05-01 Released: 2017-05-03 
• Deposition Author(s): Storer, I., Chrencik, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.201 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

PDE5A for NaV1.7

Bell, A., Bent, A., Bradley, P., Erdman, P., de Groot, M., Lewthwaite, R., Marsh, I., Ransley, S., Sciammetta, N., Smith, R., Swain, N., Torella, R., Storer, I.

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: 38.14 kDa 
• Atom Count: 3,006 
• Modeled Residue Count: 323 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-specific 3',5'-cyclic phosphodiesterase	A [auth B]	326	Homo sapiens	Mutation(s): 0  Gene Names: PDE5A, PDE5 EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O76074 (Homo sapiens) Explore O76074  Go to UniProtKB:  O76074
PHAROS:  O76074 GTEx:  ENSG00000138735

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6LK	D [auth B]	1-(5-chloro-6-methoxypyridin-3-yl)-3-methyl-N-(methylsulfonyl)-1H-indazole-5-carboxamide C16 H15 Cl N4 O4 S SOMKDSWCLVBQLT-UHFFFAOYSA-N
ZN	B, C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.201 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.84	α = 90
b = 76.1	β = 102.56
c = 80.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
BUSTER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Storer, I., Chrencik, J.

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations