2PD3

Crystal Structure of the Helicobacter pylori Enoyl-Acyl Carrier Protein Reductase in Complex with Hydroxydiphenyl Ether Compounds, Triclosan and Diclosan

• PDB DOI: https://doi.org/10.2210/pdb2PD3/pdb
• Entry: 2PD3 supersedes: 1JVF

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-31 Released: 2007-04-17 
• Deposition Author(s): Lee, H.H., Moon, J.H., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 

Starting Model: experimental

Literature

Crystal structure of the Helicobacter pylori enoyl-acyl carrier protein reductase in complex with hydroxydiphenyl ether compounds, triclosan and diclosan

Lee, H.H., Moon, J.H., Suh, S.W.

(2007) Proteins 69: 691-694

• PubMed: 17879346 
• DOI: https://doi.org/10.1002/prot.21586
• Primary Citation of Related Structures:  
  2PD3, 2PD4

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Organizational Affiliation: 

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 123.88 kDa 
• Atom Count: 8,866 
• Modelled Residue Count: 1,096 
• Deposited Residue Count: 1,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase [NADH]	A, B, C, D	275	Helicobacter pylori	Mutation(s): 0  EC: 1.3.1.9
UniProt
Find proteins for O24990 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore O24990  Go to UniProtKB:  O24990

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
TCL	F [auth A], H [auth B], J [auth C], L [auth D]	TRICLOSAN C12 H7 Cl3 O2 XEFQLINVKFYRCS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.259 
• R-Value Work: 0.233 
• R-Value Observed: 0.233 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.353	α = 90
b = 94.911	β = 106.21
c = 75.376	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-17 
Deposition Author(s): Lee, H.H., Moon, J.H., Suh, S.W.
• This entry supersedes: 1JVF

Revision History  

• Version 1.0: 2007-04-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description