5M6V

Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with a double methylated Fasudil-derivative

PDB DOI: https://doi.org/10.2210/pdb5M6V/pdb

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

Deposited: 2016-10-26 Released: 2018-06-06
Deposition Author(s): Wienen-Schmidt, B., Heine, A., Klebe, G.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.174
R-Value Work: 0.143
R-Value Observed: 0.145

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with different Fasudil-derivatives

Wienen-Schmidt, B., Jonker, H., Gerber, H.-D., Saxena, K., Kudlinzki, D., Sreeramulu, S., Heine, A., Schwalbe, H., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 43.66 kDa
Atom Count: 3,618
Modelled Residue Count: 373
Deposited Residue Count: 373
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	353	Cricetulus griseus	Mutation(s): 0 Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P25321 (Cricetulus griseus) Explore P25321 Go to UniProtKB: P25321
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25321
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens) Explore P61925 Go to UniProtKB: P61925
PHAROS: P61925 GTEx: ENSG00000171033
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61925
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
H52 Query on H52 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(S)-2-METHYL-1-[(4-METHYL-5-ISOQUINOLINE)SULFONYL]-HOMOPIPERAZINE C₁₆ H₂₁ N₃ O₂ S AWDORCFLUJZUQS-ZDUSSCGKSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.174
R-Value Work: 0.143
R-Value Observed: 0.145
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.537	α = 90
b = 73.183	β = 90
c = 108.847	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-06-06

Deposition Author(s):

Wienen-Schmidt, B.

Funding Organization	Location	Grant Number
European Research Council	Belgium	268145 - Project Acronym: DrugProfilBind

Revision History (Full details and data files)

Version 1.0: 2018-06-06
Type: Initial release
Version 1.1: 2024-01-17
Changes: Data collection, Database references, Refinement description

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.