9OFD | pdb_00009ofd

CryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimer

PDB DOI: https://doi.org/10.2210/pdb9OFD/pdb
EM Map EMD-70429: EMDB EMDataResource
NAKB: 9OFD

Classification: IMMUNE SYSTEM, HYDROLASE
Organism(s): Thermoanaerobaculum aquaticum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-04-29 Released: 2025-08-20
Deposition Author(s): Zhao, Y., Li, H.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Sequential Conformational Activation of a CARF-Fused Adenosine Deaminase by Cyclic Oligoadenylates

Zhao, Y., Li, H.

To be published.

Macromolecule Content

Total Structure Weight: 421.83 kDa
Atom Count: 21,982
Modeled Residue Count: 2,777
Deposited Residue Count: 3,754
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated ring nuclease and adenosine deaminase, subunit A	A B E [auth G] F [auth H] G [auth K] A, B, E [auth G], F [auth H], G [auth K], H [auth L]	625	Thermoanaerobaculum aquaticum	Mutation(s): 0 Gene Names: EG19_07865 EC: 3.5.4.4
UniProt
Find proteins for A0A062XY19 (Thermoanaerobaculum aquaticum) Explore A0A062XY19 Go to UniProtKB: A0A062XY19
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A062XY19
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
cA4 cleavage product, A2>P	C, D	2	Thermoanaerobaculum aquaticum
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain U [auth L] SDF format, chain R [auth K] SDF format, chain P [auth H] SDF format, chain M [auth G] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain U [auth L] MOL2 format, chain R [auth K] MOL2 format, chain P [auth H] MOL2 format, chain M [auth G] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain U [auth L] mmCIF format, chain R [auth K] mmCIF format, chain P [auth H] mmCIF format, chain M [auth G] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] M [auth G] P [auth H] R [auth K] I [auth A], K [auth B], M [auth G], P [auth H], R [auth K], U [auth L]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth G] Focus chain P [auth H] Focus chain R [auth K] Focus chain U [auth L] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth G] Focus chain P [auth H] Focus chain R [auth K] Focus chain U [auth L]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth G] SDF format, chain V [auth L] SDF format, chain T [auth K] SDF format, chain Q [auth H] SDF format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth G] MOL2 format, chain V [auth L] MOL2 format, chain T [auth K] MOL2 format, chain Q [auth H] MOL2 format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain N [auth G] mmCIF format, chain V [auth L] mmCIF format, chain T [auth K] mmCIF format, chain Q [auth H] mmCIF format, chain L [auth B]	J [auth A] L [auth B] N [auth G] Q [auth H] T [auth K] J [auth A], L [auth B], N [auth G], Q [auth H], T [auth K], V [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth G] Focus chain Q [auth H] Focus chain T [auth K] Focus chain V [auth L] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth G] Focus chain Q [auth H] Focus chain T [auth K] Focus chain V [auth L]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain S [auth K] SDF format, chain O [auth H] MOL2 format, chain S [auth K] MOL2 format, chain O [auth H] mmCIF format, chain S [auth K] mmCIF format, chain O [auth H]	O [auth H], S [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth H] Focus chain S [auth K] Interactions & Density Focus chain O [auth H] Focus chain S [auth K]