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.

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
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O24990
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
TCL Query on TCL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B]	F [auth A], H [auth B], J [auth C], L [auth D]	TRICLOSAN C₁₂ H₇ Cl₃ O₂ XEFQLINVKFYRCS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

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

View Full Validation Report

Ligand Structure Quality Assessment

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 (Full details and data files)

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

2PD3

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)