9BBF | pdb_00009bbf

Structure of Clostridioides difficile Component A (50-463) in Complex with a CDTb Oligomer

PDB DOI: https://doi.org/10.2210/pdb9BBF/pdb
EM Map EMD-44419: EMDB EMDataResource

Classification: TRANSFERASE
Organism(s): Clostridioides difficile
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-05 Released: 2024-11-27
Deposition Author(s): Sheedlo, M.J., Mullard, R.M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of Clostridioides difficile Component A (50-463) in Complex with a CDTb Oligomer

Sheedlo, M.J., Mullard, R.M.

To be published.

Macromolecule Content

Total Structure Weight: 708.21 kDa
Atom Count: 19,880
Modeled Residue Count: 2,533
Deposited Residue Count: 6,259
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyltransferase binding component	A, B, C, D, E A, B, C, D, E, F, G	835	Clostridioides difficile	Mutation(s): 0 Gene Names: cdtB
UniProt
Find proteins for A8DS70 (Clostridioides difficile) Explore A8DS70 Go to UniProtKB: A8DS70
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8DS70
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyltransferase enzymatic component	H [auth Z]	414	Clostridioides difficile	Mutation(s): 0 Gene Names: cdtA EC: 2.4.2
UniProt
Find proteins for Q9KH42 (Clostridioides difficile) Explore Q9KH42 Go to UniProtKB: Q9KH42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KH42
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain V [auth G] SDF format, chain U [auth G] SDF format, chain T [auth F] SDF format, chain S [auth F] SDF format, chain R [auth E] SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain V [auth G] MOL2 format, chain U [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain V [auth G] mmCIF format, chain U [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], S [auth F], T [auth F], U [auth G], V [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G]