4E9A | pdb_00004e9a

Structure of Peptide Deformylase form Helicobacter Pylori in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4E9A/pdb

• Classification: HYDROLASE
• 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: 1.66 Å
• R-Value Free: 
  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

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: 21.75 kDa 
• Atom Count: 1,440 
• Modeled 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
QAP	C [auth A]	2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate C17 H16 O4 SWUARLUWKZWEBQ-VQHVLOKHSA-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: 1.66 Å
• R-Value Free:  0.230 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.891	α = 90
b = 52.057	β = 90
c = 92.064	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	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: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description