5L0N

PKG I's Carboxyl Terminal Cyclic Nucleotide Binding Domain (CNB-B) in a complex with RP-cGMP

• PDB DOI: https://doi.org/10.2210/pdb5L0N/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-07-27 Released: 2017-08-02 
• Deposition Author(s): Campbell, J.C., Sankaran, B., Kim, C.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.182 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Literature

Structure of PKG I CNB-B bound to RP-cGMP

Campbell, J.C., Sankaran, B., Kim, C.W.

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: 15.67 kDa 
• Atom Count: 1,173 
• Modelled Residue Count: 127 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent protein kinase 1	A	135	Homo sapiens	Mutation(s): 0  Gene Names: PRKG1, PRKG1B, PRKGR1A, PRKGR1B EC: 2.7.11.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q13976 (Homo sapiens) Explore Q13976  Go to UniProtKB:  Q13976
PHAROS:  Q13976 GTEx:  ENSG00000185532

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6ZA	G [auth A]	2-amino-9-[(2R,4aR,6R,7R,7aS)-2,7-dihydroxy-2-sulfanylidenetetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]-3,9-dihydro-6H-purin-6-one C10 H12 N5 O6 P S JZAJZXRXCHCRMU-KVBUDSETSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 0.182 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.889	α = 90
b = 54.305	β = 90
c = 56.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Campbell, J.C., Sankaran, B., Kim, C.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM090161-02

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2019-12-25
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description