4DAW | pdb_00004daw

Crystal structure of PAK1 kinase domain with the ruthenium phthalimide complex

• PDB DOI: https://doi.org/10.2210/pdb4DAW/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-01-13 Released: 2012-03-14 
• Deposition Author(s): Maksimoska, J., Marmorstein, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.238 (Depositor) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

The art of filling protein pockets efficiently with octahedral metal complexes.

Blanck, S., Maksimoska, J., Baumeister, J., Harms, K., Marmorstein, R., Meggers, E.

(2012) Angew Chem Int Ed Engl 51: 5244-5246

• PubMed: 22383326 
• DOI: https://doi.org/10.1002/anie.201108865
• Primary Citation Related Structures: 
  4DAW

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Organizational Affiliation: 
• Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.93 kDa 
• Atom Count: 2,540 
• Modeled Residue Count: 294 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 1	A	297	Homo sapiens	Mutation(s): 1  Gene Names: PAK1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13153 (Homo sapiens) Explore Q13153  Go to UniProtKB:  Q13153
PHAROS:  Q13153 GTEx:  ENSG00000149269

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0H2	B [auth A]	[1,3-dioxo-6-(pyridin-2-yl-kappaN)-2,3-dihydro-1H-isoindol-5-yl-kappaC~5~][(thioxomethylidene)azanido-kappaN](1,4,7-trithionane-kappa~3~S~1~,S~4~,S~7~)ruthenium C20 H19 N3 O2 Ru S4 QCJZVWXEKKIDLD-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.238 (Depositor) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.676	α = 90
b = 103.549	β = 90
c = 122.79	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Maksimoska, J., Marmorstein, R.

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2012-05-30
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary