7T4W | pdb_00007t4w

Crystal Structure of cGMP-dependent Protein Kinase

PDB DOI: https://doi.org/10.2210/pdb7T4W/pdb

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

Deposited: 2021-12-10 Released: 2023-06-14
Deposition Author(s): Zebisch, M., Silvestre, L., Fischmann, T.O.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free:
0.267 (Depositor), 0.273 (DCC)
R-Value Work:
0.204 (Depositor), 0.214 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7T4W

Ligand Structure Quality Assessment

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

Literature

Selective small molecule activation of PKG1alpha: structure and function

Metwally, E., Mak, V., Sylvestre, H.L., McEwan, P., Baker, J.J., Rose, Y., Patel, A., Lim, Y.-H., Healy, D., Hanisak, J., Ermakov, G., Beaumont, M., Cheng, A.C., Greshock, T., Fischmann, T.O.

(2023) Commun Biol

Macromolecule Content

Total Structure Weight: 107.42 kDa
Atom Count: 7,688
Modeled Residue Count: 934
Deposited Residue Count: 938
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent protein kinase 1	A, B	469	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13976
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EZJ (Subject of Investigation/LOI) Query on EZJ Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	(2R)-2-({(2S,3S)-1-[(1H-benzimidazol-2-yl)methyl]-2-phenylpiperidin-3-yl}oxy)-2-(3,5-dichlorophenyl)ethan-1-ol C₂₇ H₂₇ Cl₂ N₃ O₂ BBVDAZWVTVADSO-KLJDGLGGSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A, B	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.23 Å
R-Value Free: 0.267 (Depositor), 0.273 (DCC)
R-Value Work: 0.204 (Depositor), 0.214 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93	α = 90
b = 102.621	β = 90
c = 104.028	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction
STARANISO	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Fischmann, T.O.

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2023-07-12
Changes: Data collection, Database references
Version 1.2: 2024-11-06
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.