5LCR | pdb_00005lcr

Cocrystal structure of cAMP-dependent Protein Kinase (PKA) in complex with open-chain Fasudil-derivative (Ligand 04)

PDB DOI: https://doi.org/10.2210/pdb5LCR/pdb

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

Deposited: 2016-06-22 Released: 2018-01-17
Deposition Author(s): Wienen-Schmidt, B., Heine, A., Klebe, G.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.155 (Depositor), 0.159 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

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

Wienen, B., Jonker, H.R.A., Wulsdorf, T., Gerber, H.-D., Saxena, K., Kudlinzki, D., Sreeramulu, S., Parigi, G., Luchinat, C., Heine, A., Schwalbe, H., Klebe, G.

To be published.

Macromolecule Content

Total Structure Weight: 43.91 kDa
Atom Count: 3,444
Modeled Residue Count: 372
Deposited Residue Count: 373
Unique protein chains: 2

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61925
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6TX Query on 6TX 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]	2-[isoquinolin-5-ylsulfonyl(propyl)amino]ethylazanium C₁₄ H₂₀ N₃ O₂ S KYMSHJLROPBLLU-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MOH Query on MOH Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B]	METHANOL C H₄ O OKKJLVBELUTLKV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B]

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: 1.56 Å
R-Value Free: 0.197 (Depositor), 0.200 (DCC)
R-Value Work: 0.155 (Depositor), 0.159 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.279	α = 90
b = 72.84	β = 90
c = 108.727	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

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-01-17

Deposition Author(s):

Wienen-Schmidt, B.

Heine, A.

Klebe, G.

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

Revision History (Full details and data files)

Version 1.0: 2018-01-17
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary