9CKP | pdb_00009ckp

Human G protein-coupled receptor kinase 5-D311N in complex with sangivamycin

• PDB DOI: https://doi.org/10.2210/pdb9CKP/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-07-09 Released: 2025-07-16 
• Deposition Author(s): Chen, Y., Tesmer, J.J.G.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.270 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Structures of G protein-coupled receptor kinase 5 in multiple conformations reveals mechanism of activation and inhibition

Chen, Y., Tesmer, J.J.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.32 kDa 
• Atom Count: 4,445 
• Modeled Residue Count: 538 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G protein-coupled receptor kinase 5	A	598	Homo sapiens	Mutation(s): 1  Gene Names: GRK5 EC: 2.7.11.16
UniProt & NIH Common Fund Data Resources
Find proteins for P34947 (Homo sapiens) Explore P34947  Go to UniProtKB:  P34947
PHAROS:  P34947 GTEx:  ENSG00000198873

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SGV (Subject of Investigation/LOI)	C [auth A]	SANGIVAMYCIN C12 H15 N5 O5 OBZJZDHRXBKKTJ-JTFADIMSSA-N
ACE (Subject of Investigation/LOI)	B [auth A]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N
K (Subject of Investigation/LOI)	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.270 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.206	α = 90
b = 140.206	β = 90
c = 77.832	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Chen, Y., Tesmer, J.J.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL071818

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release