2KMN

Solution structure of peptide deformylase complexed with actinonin

• PDB DOI: https://doi.org/10.2210/pdb2KMN/pdb

• Classification: HYDROLASE/ANTIBIOTIC
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-08-01 Released: 2009-08-25 
• Deposition Author(s): McElroy, C.A., Amero, C.D., Byerly, D.W., Foster, M.P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution Structure of Peptide Deformylase complexed with Actinonin

McElroy, C.A., Amero, C.D., Byerly, D.W., Foster, M.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.11 kDa 
• Atom Count: 1,194 
• Modelled Residue Count: 147 
• Deposited Residue Count: 147 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase	A	147	Escherichia coli K-12	Mutation(s): 0  Gene Names: def, fms, b3287, JW3248 EC: 3.5.1.88
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12)) Explore P0A6K3  Go to UniProtKB:  P0A6K3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	C [auth A]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BB2	BindingDB:  2KMN	IC50: min: 6, max: 140 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-25 
Deposition Author(s): McElroy, C.A., Amero, C.D., Byerly, D.W., Foster, M.P.

Revision History  

• Version 1.0: 2009-08-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Database references, Derived calculations