4EZS

Crystal structure of the substrate binding domain of E.coli DnaK in complex with metchnikowin (residues 20 to 26)

• PDB DOI: https://doi.org/10.2210/pdb4EZS/pdb

• Classification: CHAPERONE/PEPTIDE BINDING PROTEIN
• Organism(s): Escherichia coli K-12, Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-03 Released: 2013-04-24 
• Deposition Author(s): Zahn, M., Straeter, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Structural studies of DnaK in complex with proline rich antimicrobial peptides reveal two different peptide binding modes

Zahn, M., Straeter, N.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A4B4 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B1C1D1E1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.88 kDa 
• Atom Count: 1,821 
• Modelled Residue Count: 226 
• Deposited Residue Count: 227 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein DnaK	A	219	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0014, dnaK, groP, grpF, JW0013, seg
UniProt
Find proteins for P0A6Y8 (Escherichia coli (strain K12)) Explore P0A6Y8  Go to UniProtKB:  P0A6Y8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Metchnikowin	B	8	Drosophila melanogaster	Mutation(s): 0
UniProt
Find proteins for Q24395 (Drosophila melanogaster) Explore Q24395  Go to UniProtKB:  Q24395

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.256 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.437	α = 90
b = 116.905	β = 90
c = 36.994	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Zahn, M., Straeter, N.

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations