9FOL | pdb_00009fol

Succinyl-CoA:(R)-benzylsuccinate CoA-transferase (BbsEF), D178-CoA adduct + succinate (weakly occupied)

PDB DOI: https://doi.org/10.2210/pdb9FOL/pdb

Classification: TRANSFERASE
Organism(s): Aromatoleum aromaticum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-12 Released: 2025-12-24
Deposition Author(s): Ermler, U., Heider, J., Demmer, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.213 (Depositor), 0.217 (DCC)
R-Value Work:
0.183 (Depositor), 0.189 (DCC)
R-Value Observed:
0.185 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the succinyl-CoA:(R)-benzylsuccinate CoA-transferase

Schuehle, K., Demmer, U., Heider, J., Ermler, U.

To be published.

Macromolecule Content

Total Structure Weight: 184.29 kDa
Atom Count: 13,732
Modeled Residue Count: 1,624
Deposited Residue Count: 1,638
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit of Benzylsuccinate CoA-transferase	A, C	410	Aromatoleum aromaticum	Mutation(s): 0 Gene Names: bbsE, c2A312
UniProt
Find proteins for Q5P687 (Aromatoleum aromaticum (strain DSM 19018 / LMG 30748 / EbN1)) Explore Q5P687 Go to UniProtKB: Q5P687
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5P687
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Subunit of Benzylsuccinate CoA-transferase	B, D	409	Aromatoleum aromaticum	Mutation(s): 0 Gene Names: bbsF, c2A311
UniProt
Find proteins for Q5P688 (Aromatoleum aromaticum (strain DSM 19018 / LMG 30748 / EbN1)) Explore Q5P688 Go to UniProtKB: Q5P688
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5P688
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain T [auth D] MOL2 format, chain I [auth B] MOL2 format, chain T [auth D] mmCIF format, chain I [auth B] mmCIF format, chain T [auth D]	I [auth B], T [auth D]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain I [auth B] Focus chain T [auth D] Interactions & Density Focus chain I [auth B] Focus chain T [auth D]
PGE (Subject of Investigation/LOI) Query on PGE Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain F [auth A]	F [auth A] L [auth B] M [auth C] N [auth C] V [auth D] F [auth A], L [auth B], M [auth C], N [auth C], V [auth D], W [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain V [auth D] Focus chain W [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain U [auth D] MOL2 format, chain J [auth B] MOL2 format, chain U [auth D] mmCIF format, chain J [auth B] mmCIF format, chain U [auth D]	J [auth B], U [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain J [auth B] Focus chain U [auth D] Interactions & Density Focus chain J [auth B] Focus chain U [auth D]
SIN (Subject of Investigation/LOI) Query on SIN Download Ideal Coordinates CCD File SDF format, chain Z [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Z [auth D]	Z [auth D]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain Z [auth D] Interactions & Density Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth D]	E [auth A] G [auth A] H [auth B] K [auth B] O [auth C] E [auth A], G [auth A], H [auth B], K [auth B], O [auth C], P [auth C], Q [auth C], R [auth D], S [auth D], X [auth D], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain X [auth D] Focus chain Y [auth D]