9KRV | pdb_00009krv

B. bacteriovorus MaeB acetyl-CoA bound form

PDB DOI: https://doi.org/10.2210/pdb9KRV/pdb
EM Map EMD-62542: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Bdellovibrio bacteriovorus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-28 Released: 2025-12-03
Deposition Author(s): Sassa, M., Yamato, H., Tanino, H., Fukuda, Y., Inoue, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.18 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

Malic enzymes from different bacteria evolved distinct effector binding sites showing the same allosteric regulation mechanism

Sassa, M., Yamato, H., Tanino, H., Fukuda, Y., Inoue, T.

To be published.

Macromolecule Content

Total Structure Weight: 517.4 kDa
Atom Count: 22,847
Modeled Residue Count: 2,888
Deposited Residue Count: 4,656
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent malic enzyme	A, B, C, D, E A, B, C, D, E, F	776	Bdellovibrio bacteriovorus	Mutation(s): 0 Gene Names: B9G79_09885
UniProt
Find proteins for A0A1Z3N8R4 (Bdellovibrio bacteriovorus) Explore A0A1Z3N8R4 Go to UniProtKB: A0A1Z3N8R4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1Z3N8R4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACO (Subject of Investigation/LOI) Query on ACO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain R [auth F] SDF format, chain S [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] MOL2 format, chain S [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F] mmCIF format, chain S [auth F]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], R [auth F], S [auth F]	*ACETYL COENZYME A** C₂₃ H₃₈ N₇ O₁₇ P₃ S ZSLZBFCDCINBPY-ZSJPKINUSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain R [auth F] Focus chain S [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain R [auth F] Focus chain S [auth F]
NAP (Subject of Investigation/LOI) Query on NAP Download Ideal Coordinates CCD File SDF format, chain Q [auth E] SDF format, chain T [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain T [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain T [auth F]	Q [auth E], T [auth F]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain Q [auth E] Focus chain T [auth F] Interactions & Density Focus chain Q [auth E] Focus chain T [auth F]