1XQZ | pdb_00001xqz

Crystal Structure of hPim-1 kinase at 2.1 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.297 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.249 (Depositor), 0.240 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1XQZ

This is version 1.5 of the entry. See complete history

Literature

Structural Basis of Constitutive Activity and a Unique Nucleotide Binding Mode of Human Pim-1 Kinase.

Qian, K.C.Wang, L.Hickey, E.R.Studts, J.Barringer, K.Peng, C.Kronkaitis, A.Li, J.White, A.Mische, S.Farmer, B.

(2005) J Biological Chem 280: 6130-6137

  • DOI: https://doi.org/10.1074/jbc.M409123200
  • Primary Citation Related Structures: 
    1XQZ, 1XR1

  • PubMed Abstract: 

    Pim-1 kinase is a member of a distinct class of serine/threonine kinases consisting of Pim-1, Pim-2, and Pim-3. Pim kinases are highly homologous to one another and share a unique consensus hinge region sequence, ER-PXPX, with its two proline residues separated by a non-conserved residue, but they (Pim kinases) have <30% sequence identity with other kinases. Pim-1 has been implicated in both cytokine-induced signal transduction and the development of lymphoid malignancies. We have determined the crystal structures of apo Pim-1 kinase and its AMP-PNP (5'-adenylyl-beta,gamma-imidodiphosphate) complex to 2.1-angstroms resolutions. The structures reveal the following. 1) The kinase adopts a constitutively active conformation, and extensive hydrophobic and hydrogen bond interactions between the activation loop and the catalytic loop might be the structural basis for maintaining such a conformation. 2) The hinge region has a novel architecture and hydrogen-bonding pattern, which not only expand the ATP pocket but also serve to establish unambiguously the alignment of the Pim-1 hinge region with that of other kinases. 3) The binding mode of AMP-PNP to Pim-1 kinase is unique and does not involve a critical hinge region hydrogen bond interaction. Analysis of the reported Pim-1 kinase-domain structures leads to a hypothesis as to how Pim kinase activity might be regulated in vivo.


  • Organizational Affiliation
    • Departments of Medicinal Chemistry and Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., Research and Development, 175 Briar Ridge Rd., Ridgefield, CT 06877, USA.

Macromolecule Content 

  • Total Structure Weight: 34.25 kDa 
  • Atom Count: 2,317 
  • Modeled Residue Count: 277 
  • Deposited Residue Count: 300 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase Pim-1300Homo sapiensMutation(s): 0 
Gene Names: PIM1
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.297 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.249 (Depositor), 0.240 (DCC) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.9α = 90
b = 95.9β = 90
c = 79.96γ = 120
Software Package:
Software NamePurpose
CNXrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2018-01-31
    Changes: Experimental preparation
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references