2IWI

CRYSTAL STRUCTURE OF THE HUMAN PIM2 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU1

• PDB DOI:  https://doi.org/10.2210/pdb2IWI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-06-30 Released: 2006-08-02 
• Deposition Author(s): Russo, S., Debreczeni, J.E., Amos, A., Bullock, A.N., Fedorov, O., Niesen, F., Sobott, F., Turnbull, A., Pike, A.C.W., Ugochukwu, E., Papagrigoriou, E., Bunkoczi, G., Gorrec, F., Edwards, A., Arrowsmith, C., Weigelt, J., Sundstrom, M., von Delft, F., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 

Literature

Crystal structure of the PIM2 kinase in complex with an organoruthenium inhibitor.

Bullock, A.N., Russo, S., Amos, A., Pagano, N., Bregman, H., Debreczeni, J.E., Lee, W.H., von Delft, F., Meggers, E., Knapp, S.

(2009) PLoS One 4: e7112-e7112

• PubMed: 19841674 
• DOI: https://doi.org/10.1371/journal.pone.0007112
• Primary Citation of Related Structures:  
  2IWI


• PubMed Abstract: 
  

  The serine/threonine kinase PIM2 is highly expressed in human leukemia and lymphomas and has been shown to positively regulate survival and proliferation of tumor cells. Its diverse ATP site makes PIM2 a promising target for the development of anticancer agents. To date our knowledge of catalytic domain structures of the PIM kinase family is limited to PIM1 which has been extensively studied and which shares about 50% sequence identity with PIM2.

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Organizational Affiliation: 

University of Oxford, Structural Genomics Consortium, Oxford, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 69.59 kDa 
• Atom Count: 3,746 
• Modelled Residue Count: 493 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE PIM-2	A, B	312	Homo sapiens	Mutation(s): 0  Gene Names: PIM2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P1W9 (Homo sapiens) Explore Q9P1W9  Go to UniProtKB:  Q9P1W9
PHAROS:  Q9P1W9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HB1	C [auth A], D [auth B]	RUTHENIUM-PYRIDOCARBAZOLE-1 C23 H13 N3 O3 Ru HQDDSWVENMEGOZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.289 
• R-Value Work: 0.242 
• R-Value Observed: 0.244 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.07	α = 90
b = 153.07	β = 90
c = 78.6	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-02 
Deposition Author(s): Russo, S., Debreczeni, J.E., Amos, A., Bullock, A.N., Fedorov, O., Niesen, F., Sobott, F., Turnbull, A., Pike, A.C.W., Ugochukwu, E., Papagrigoriou, E., Bunkoczi, G., Gorrec, F., Edwards, A., Arrowsmith, C., Weigelt, J., Sundstrom, M., von Delft, F., Knapp, S.

Revision History  

• Version 1.0: 2006-08-02
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.4: 2018-02-28
  Changes: Database references, Source and taxonomy
• Version 1.5: 2019-05-08
  Changes: Data collection, Experimental preparation