7KZI

Intermediate state (QQQ) of near full-length DnaK alternatively fused with a substrate peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Intermediates in allosteric equilibria of DnaK-ATP interactions with substrate peptides

Wang, W.Hendrickson, W.A.

(2021) Acta Crystallogr D Biol Crystallogr 77: 606-617


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein DnaK fused with substrate peptide,Chaperone protein DnaK fused with substrate peptide
A, B
628Escherichia coli K-12Mutation(s): 1 
Gene Names: dnaKFAZ83_07380
UniProt
Find proteins for P0A6Y8 (Escherichia coli (strain K12))
Explore P0A6Y8 
Go to UniProtKB:  P0A6Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6Y8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.256 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.518α = 90
b = 121.518β = 90
c = 457.878γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM107462

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description