9X75 | pdb_00009x75

Crystal structure of Campylobacter jejuni DapE in complex with captopril

• PDB DOI: https://doi.org/10.2210/pdb9X75/pdb

• Classification: HYDROLASE
• Organism(s): Campylobacter jejuni
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-10-16 Released: 2026-10-28 
• Deposition Author(s): Ahn, S.Y., You, Y.B., Yoon, S.I.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: in silico

Literature

Structural analysis of the putative succinyl-diaminopimelic acid desuccinylase DapE from Campylobacter jejuni

Yoon, S.I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 82.94 kDa 
• Atom Count: 5,631 
• Modeled Residue Count: 732 
• Deposited Residue Count: 742 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Succinyl-diaminopimelate desuccinylase	A, B	371	Campylobacter jejuni	Mutation(s): 0  Gene Names: dapE, Cj1048c EC: 3.5.1.18
UniProt
Find proteins for Q0P9K4 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0P9K4  Go to UniProtKB:  Q0P9K4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X8Z	E [auth A], H [auth B]	L-CAPTOPRIL C9 H15 N O3 S FAKRSMQSSFJEIM-RQJHMYQMSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.224 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.717	α = 90
b = 117.361	β = 90
c = 197.778	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Ahn, S.Y., You, Y.B., Yoon, S.I.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	RS-2023-00208153

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release