8SSK

Citrobacter rodentium contact dependent growth inhibition (CDI) entry and toxin (CdiA-CT) domains

PDB DOI: https://doi.org/10.2210/pdb8SSK/pdb

Classification: TOXIN
Organism(s): Citrobacter rodentium
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-05-08 Released: 2024-05-15
Deposition Author(s): Cuthbert, B.J., Goulding, C.W., Hayes, C.S., Nhan, D.Q.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.186
R-Value Work: 0.162
R-Value Observed: 0.164

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Citrobacter rodentium contact dependent growth inhibition (CDI) entry and toxin (CdiA-CT) domains

Cuthbert, B.J., Goulding, C.W., Hayes, C.S., Nhan, D.Q.

To be published.

Macromolecule Content

Total Structure Weight: 136.69 kDa
Atom Count: 10,327
Modelled Residue Count: 1,220
Deposited Residue Count: 1,272
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Contact-dependent inhibitor A	A, B, C, D	318	Citrobacter rodentium	Mutation(s): 1 Gene Names: stbD, E2R62_11320
UniProt
Find proteins for A0A482PFX0 (Citrobacter rodentium) Explore A0A482PFX0 Go to UniProtKB: A0A482PFX0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A482PFX0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain E [auth A] SDF format, chain J [auth A] SDF format, chain R [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth A] MOL2 format, chain R [auth C]	BA [auth C], E [auth A], J [auth A], R [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth C] Focus chain E [auth A] Focus chain J [auth A] Focus chain R [auth C] Interactions & Density Focus chain BA [auth C] Focus chain E [auth A] Focus chain J [auth A] Focus chain R [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C]	AA [auth C] F [auth A] FA [auth D] GA [auth D] H [auth A] AA [auth C], F [auth A], FA [auth D], GA [auth D], H [auth A], HA [auth D], IA [auth D], N [auth B], O [auth B], P [auth B], S [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Interactions & Density Focus chain AA [auth C] Focus chain F [auth A] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain JA [auth D] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	DA [auth D] EA [auth D] G [auth A] I [auth A] JA [auth D] DA [auth D], EA [auth D], G [auth A], I [auth A], JA [auth D], L [auth B], M [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C], Z [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain I [auth A] Focus chain JA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain I [auth A] Focus chain JA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain Q [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain Q [auth B]	CA [auth C], K [auth A], KA [auth D], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain Q [auth B] Interactions & Density Focus chain CA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain Q [auth B]