2BIK

Human Pim1 phosphorylated on Ser261

• PDB DOI: https://doi.org/10.2210/pdb2BIK/pdb

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


• Deposited: 2005-01-22 Released: 2005-02-07 
• Deposition Author(s): Knapp, S., Debreczeni, J., Bullock, A., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Guo, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.183 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Human Pim1 Phosphorylated on Ser261

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

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 36.2 kDa 
• Atom Count: 2,580 
• Modelled 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 PIM-1	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BI1	B	3-{1-[3-(DIMETHYLAMINO)PROPYL]-1H-INDOL-3-YL}-4-(1H-INDOL-3-YL)-1H-PYRROLE-2,5-DIONE C25 H24 N4 O2 QMGUOJYZJKLOLH-UHFFFAOYSA-N
CL	C [auth B], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-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

Binding Affinity Annotations
ID	Source	Binding Affinity
BI1	BindingDB:  2BIK	Kd: 10 (nM) from 1 assay(s)
		IC50: min: 27, max: 150 (nM) from 2 assay(s)
		-TΔS: 16.08 (kJ/mol) from 1 assay(s)
		ΔG: -4.35e+1 (kJ/mol) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.183 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.321	α = 90
b = 99.321	β = 90
c = 80.123	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: 2005-02-07 
Deposition Author(s): Knapp, S., Debreczeni, J., Bullock, A., von Delft, F., Sundstrom, M., Arrowsmith, C., Edwards, A., Guo, K.

Revision History  

• Version 1.0: 2005-02-07
  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: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 1.5: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.6: 2019-10-23
  Changes: Data collection, Database references, Other
• Version 1.7: 2023-12-13
  Changes: Data collection, Database references, Refinement description
• Version 1.8: 2024-11-20
  Changes: Structure summary