1XWS | pdb_00001xws

Crystal Structure of the human PIM1 kinase domain

• PDB DOI: https://doi.org/10.2210/pdb1XWS/pdb

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


• Deposited: 2004-11-02 Released: 2004-11-16 
• 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: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal structure of human PIM1 kinase domain

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.

Macromolecule Content 

• Total Structure Weight: 36.24 kDa 
• Atom Count: 2,510 
• 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 Pim-1	A	313	Homo sapiens	Mutation(s): 0  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	C [auth A]	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
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
BI1	BindingDB:  1XWS	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:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.55	α = 90
b = 99.55	β = 90
c = 80.06	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-16 
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: 2004-11-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations