23PY | pdb_000023py

N-His tagged YghJ protein substrate-accessible state

PDB DOI: https://doi.org/10.2210/pdb23PY/pdb
EM Map EMD-69161: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-02-12 Released: 2026-09-02
Deposition Author(s): Gu, J.K., Zhang, M.H.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 23PY

This is version 1.0 of the entry. See complete history.

Literature

Molecular basis for zymogen-like autoinhibition of the M60-like metallopeptidase YghJ.

Zhang, M., Wu, B., Liang, Z., Su, Y., Peng, H., Gu, J.

(2026) Protein Cell

PubMed: 42629342 Search on PubMed
DOI: https://doi.org/10.1093/procel/pwag059
Primary Citation Related Structures:
23PX, 23PY, 23PZ

Organizational Affiliation

Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University Medical School, Shenzhen 518055, China.

Macromolecule Content

Total Structure Weight: 167.47 kDa
Atom Count: 8,474
Modeled Residue Count: 1,079
Deposited Residue Count: 1,520
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lipoprotein AcfD homolog	A	1,520	Escherichia coli K-12	Mutation(s): 0 Gene Names: yghJ, b4466, JW5925, ECK2968
UniProt
Find proteins for P0CK95 (Escherichia coli (strain K12)) Explore P0CK95 Go to UniProtKB: P0CK95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CK95
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	RELION	4

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32270832

Revision History (Full details and data files)

Version 1.0: 2026-09-02
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.