4EZS | pdb_00004ezs

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.256 (Depositor), 0.255 (DCC)
R-Value Work:
0.199 (Depositor), 0.197 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4EZS

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A6Y8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
UniProt Group	Q24395
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.256 (Depositor), 0.255 (DCC)
R-Value Work: 0.199 (Depositor), 0.197 (DCC)
R-Value Observed: 0.201 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-04-24

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.