6BG2

Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain in AMP-PNP bound state

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2017-10-27 Released: 2018-10-31 
  • Deposition Author(s): Qin, L., Sankaran, B., Kim, C.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain

Qin, L., Sankaran, B., Casteel, D., Kim, C.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-dependent protein kinase 1A [auth C],
B,
C [auth A],
D		347Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13976
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
Download Ideal Coordinates CCD File 
E [auth C],
H [auth B],
K [auth A],
N [auth D]		PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MN
Query on MN
Download Ideal Coordinates CCD File 
F [auth C]
G [auth C]
I [auth B]
J [auth B]
L [auth A]
F [auth C],
G [auth C],
I [auth B],
J [auth B],
L [auth A],
M [auth A],
O [auth D],
P [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO		A [auth C],
B,
C [auth A],
D		L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.39α = 90
b = 98.5β = 133.47
c = 116.424γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM090161-08

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description