9UKF | pdb_00009ukf

CryoEM structure of Brucella melitensis CobS(E142Q)-CobT complex with ATP (conformation 1)

PDB DOI: https://doi.org/10.2210/pdb9UKF/pdb
EM Map EMD-64237: EMDB EMDataResource

Classification: LIGASE
Organism(s): Brucella melitensis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-04-17 Released: 2026-07-29
Deposition Author(s): Zhou, Y.L., Chen, X., Liu, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Assembly of the ATP-driven cobalt chelatase

Zhou, Y.L., Yuan, H., Wu, Y.C., Wang, J., Chen, H., Yao, L., Wang, M., Wang, X., Wang, J., He, C., Chen, X., Liu, L.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.07.21.739949

Macromolecule Content

Total Structure Weight: 435.94 kDa
Atom Count: 20,302
Modeled Residue Count: 2,577
Deposited Residue Count: 3,879
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobaltochelatase subunit CobS	A [auth E] B [auth F] F [auth A] G [auth B] H [auth C] A [auth E], B [auth F], F [auth A], G [auth B], H [auth C], I [auth D]	328	Brucella melitensis	Mutation(s): 1 Gene Names: BI318_03735 EC: 6.6.1.2
UniProt
Find proteins for A0AB36PZV1 (Brucella melitensis) Explore A0AB36PZV1 Go to UniProtKB: A0AB36PZV1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AB36PZV1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cobaltochelatase subunit CobT	C [auth G], D [auth a], E [auth c]	637	Brucella melitensis	Mutation(s): 0 Gene Names: BI318_03740 EC: 6.6.1.2
UniProt
Find proteins for A0AB36PXH5 (Brucella melitensis) Explore A0AB36PXH5 Go to UniProtKB: A0AB36PXH5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AB36PXH5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 S [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain L [auth F] SDF format, chain J [auth E] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain L [auth F] MOL2 format, chain J [auth E] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain L [auth F] mmCIF format, chain J [auth E]	J [auth E] L [auth F] N [auth A] P [auth B] Q [auth C] J [auth E], L [auth F], N [auth A], P [auth B], Q [auth C], S [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain J [auth E] Focus chain L [auth F] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain S [auth D] Interactions & Density Focus chain J [auth E] Focus chain L [auth F] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain S [auth D]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain R [auth C] SDF format, chain O [auth A] SDF format, chain M [auth F] SDF format, chain K [auth E] MOL2 format, chain T [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth A] MOL2 format, chain M [auth F] MOL2 format, chain K [auth E] mmCIF format, chain T [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth A] mmCIF format, chain M [auth F] mmCIF format, chain K [auth E]	K [auth E], M [auth F], O [auth A], R [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth E] Focus chain M [auth F] Focus chain O [auth A] Focus chain R [auth C] Focus chain T [auth D] Interactions & Density Focus chain K [auth E] Focus chain M [auth F] Focus chain O [auth A] Focus chain R [auth C] Focus chain T [auth D]