1I5D

STRUCTURE OF CHEA DOMAIN P4 IN COMPLEX WITH TNP-ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

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Ligand Structure Quality Assessment 


This is version 1.3 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: 10.1038/86243
  • Primary Citation of 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+) ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CHEMOTAXIS PROTEIN CHEAA191Thermotoga maritimaMutation(s): 0 
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
128 (Subject of Investigation/LOI)
Query on 128

Download Ideal Coordinates CCD File 
D [auth A]SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE
C16 H17 N8 O19 P3
XFMMHXLUHKBKQE-UHEGPQQHSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
128 PDBBind:  1I5D Kd: 10 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.19α = 90
b = 85.19β = 90
c = 73.77γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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: 2015-09-23
    Changes: Non-polymer description