22IR | pdb_000022ir

Cryo-EM Structure of Dimeric EcCaspase Bound to N7-cADPR

PDB DOI: https://doi.org/10.2210/pdb22IR/pdb
EM Map EMD-68347: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2026-01-13 Released: 2026-11-04
Deposition Author(s): Hao, F., Xin, X.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM Structure of Dimeric EcCaspase Bound to N7-cADPR

Hao, F., Xin, X.

To be published.

Macromolecule Content

Total Structure Weight: 71.79 kDa
Atom Count: 4,323
Modeled Residue Count: 546
Deposited Residue Count: 642
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase family protein	A [auth B], B [auth A]	321	Escherichia coli	Mutation(s): 0 Gene Names: QDW62_21060 EC: 3.4.22
UniProt
Find proteins for A0AAF0KJ23 (Escherichia coli) Explore A0AAF0KJ23 Go to UniProtKB: A0AAF0KJ23
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAF0KJ23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EZF (Subject of Investigation/LOI) Query on A1EZF Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	Adenosine 5'-diphosphate-cyclo[N7:1'']-ribose C₁₅ H₂₃ N₅ O₁₃ P₂ YTHNJUITAOGVDA-KEOHHSTQSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release