2BZI | pdb_00002bzi

CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU2

• PDB DOI: https://doi.org/10.2210/pdb2BZI/pdb

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


• Deposited: 2005-08-18 Released: 2005-12-08 
• Deposition Author(s): Debreczeni, J.E., Bullock, A., Knapp, S., von Delft, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Human Pim1 in Complex with Ruthenium Organometallic Ligands

Debreczeni, J.E., Bullock, A., Knapp, S., von Delft, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 36.21 kDa 
• Atom Count: 2,555 
• Modeled Residue Count: 273 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTO-ONCOGENE SERINE THREONINE PROTEIN KINASE PIM1	A [auth B]	313	Homo sapiens	Mutation(s): 1  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens) Explore P11309  Go to UniProtKB:  P11309
PHAROS:  P11309 GTEx:  ENSG00000137193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DW2	B	RU-PYRIDOCARBAZOLE-2 C23 H13 N3 O4 Ru KERGYDCAYYYADM-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A [auth B]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.265 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.241	α = 90
b = 98.241	β = 90
c = 80.891	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-08 
Deposition Author(s): Debreczeni, J.E., Bullock, A., Knapp, S., von Delft, F., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A.

Revision History  

• Version 1.0: 2005-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.5: 2024-11-13
  Changes: Structure summary