4E9B

Structure of Peptide Deformylase form Helicobacter Pylori in complex with actinonin

• PDB DOI: https://doi.org/10.2210/pdb4E9B/pdb

• Classification: HYDROLASE/HYDROLASE INHIBTIOR
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-20 Released: 2013-04-24 
• Deposition Author(s): Cui, K., Zhu, L., Lu, W., Huang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.220 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Identification of Novel Peptide Deformylase Inhibitors from Natural Products

Cui, K., Zhu, L., Lu, W., Huang, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.85 kDa 
• Atom Count: 1,423 
• Modelled Residue Count: 163 
• Deposited Residue Count: 181 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide deformylase 11	A	181	Helicobacter pylori	Mutation(s): 0  Gene Names: def, def11 EC: 3.5.1.88
UniProt
Find proteins for Q672W7 (Helicobacter pylori) Explore Q672W7  Go to UniProtKB:  Q672W7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BB2	C [auth A]	ACTINONIN C19 H35 N3 O5 XJLATMLVMSFZBN-VYDXJSESSA-N
EPE	D [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
DMS	E [auth A], F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.220 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.394	α = 90
b = 51.779	β = 90
c = 91.074	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Cui, K., Zhu, L., Lu, W., Huang, J.

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations