1I58 | pdb_00001i58

STRUCTURE OF THE HISTIDINE KINASE CHEA ATP-BINDING DOMAIN IN COMPLEX WITH ATP ANALOG ADPCP AND MAGNESIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.262 (Depositor) 
  • R-Value Work: 
    0.223 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.223 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Nucleotide binding by the histidine kinase CheA.

Bilwes, A.M.Quezada, C.M.Croal, L.R.Crane, B.R.Simon, M.I.

(2001) Nat Struct Biol 8: 353-360

  • DOI: https://doi.org/10.1038/86243
  • Primary Citation Related Structures: 
    1I58, 1I59, 1I5A, 1I5B, 1I5C, 1I5D

  • PubMed Abstract: 

    To probe the structural basis for protein histidine kinase (PHK) catalytic activity and the prospects for PHK-specific inhibitor design, we report the crystal structures for the nucleotide binding domain of Thermotoga maritima CheA with ADP and three ATP analogs (ADPNP, ADPCP and TNP-ATP) bound with either Mg(2+) or Mn(2+). The conformation of ADPNP bound to CheA and related ATPases differs from that reported in the ADPNP complex of PHK EnvZ. Interactions of the active site with the nucleotide gamma-phosphate and its associated Mg(2+) ion are linked to conformational changes in an ATP-lid that could mediate recognition of the substrate domain. The inhibitor TNP-ATP binds CheA with its phosphates in a nonproductive conformation and its adenine and trinitrophenyl groups in two adjacent binding pockets. The trinitrophenyl interaction may be exploited for designing CheA-targeted drugs that would not interfere with host ATPases.


  • Organizational Affiliation
    • Division of Biology, California Institute of Technology, 1200 East California Blvd., Pasadena, California 91125, USA.

Macromolecule Content 

  • Total Structure Weight: 43.23 kDa 
  • Atom Count: 3,160 
  • Modeled Residue Count: 364 
  • Deposited Residue Count: 378 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CHEMOTAXIS PROTEIN CHEA
A, B
189Thermotoga maritimaMutation(s): 3 
EC: 2.7.3 (PDB Primary Data), 2.7.13.3 (UniProt)
UniProt
Find proteins for Q56310 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q56310 
Go to UniProtKB:  Q56310
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56310
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.262 (Depositor) 
  • R-Value Work:  0.223 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.223 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.82α = 90
b = 48.93β = 103.54
c = 77.04γ = 90
Software Package:
Software NamePurpose
EPMRphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-09
    Changes: Data collection, Refinement description