9PL0 | pdb_00009pl0

The structure of the Fusobacterium nucleatum Enoyl-Acyl Carrier Protein Reductase (FabK) bound to an inhibitor

PDB DOI: https://doi.org/10.2210/pdb9PL0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Fusobacterium nucleatum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-15 Released: 2026-01-28
Deposition Author(s): Alaidi, O., Avad, K., Hevener, K.
Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.254 (Depositor), 0.254 (DCC)
R-Value Work:
0.213 (Depositor), 0.214 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and Biochemical Characterization of Fusobacterium nucleatum Enoyl-ACP Reductase II (FabK) Reveals the Basis for Bacterial Species-Specific Inhibition

Avad, K., Alaidi, O., Okpomo, D., Pavel, F.B.A., Doran, D., Matheson, M., Sun, D., Hurdle, J., Hevener, K.E.

(2025) ACS Bio Med Chem Au

DOI: https://doi.org/10.1021/acsbiomedchemau.5c00199

Macromolecule Content

Total Structure Weight: 457.36 kDa
Atom Count: 30,074
Modeled Residue Count: 3,777
Deposited Residue Count: 4,056
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-[acyl-carrier-protein] reductase	A B C D E A, B, C, D, E, F, G [auth J], H [auth G], I [auth H], J [auth I], K, L	338	Fusobacterium nucleatum	Mutation(s): 0 Gene Names: FN0174 EC: 1.3.1.9
UniProt
Find proteins for Q8RGV3 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8RGV3 Go to UniProtKB: Q8RGV3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RGV3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JEF Query on JEF Download Ideal Coordinates CCD File SDF format, chain BC [auth I] SDF format, chain EA [auth C] SDF format, chain HC [auth K] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PB [auth G] SDF format, chain S [auth A] SDF format, chain UA [auth E] SDF format, chain WA [auth E] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain VB [auth H] SDF format, chain VA [auth E] SDF format, chain T [auth A] SDF format, chain KB [auth J] SDF format, chain DB [auth F] MOL2 format, chain BC [auth I] MOL2 format, chain EA [auth C] MOL2 format, chain HC [auth K] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PB [auth G] MOL2 format, chain S [auth A] MOL2 format, chain UA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain VB [auth H] MOL2 format, chain VA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain KB [auth J] MOL2 format, chain DB [auth F] mmCIF format, chain BC [auth I] mmCIF format, chain EA [auth C] mmCIF format, chain HC [auth K] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain PB [auth G] mmCIF format, chain S [auth A] mmCIF format, chain UA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain VB [auth H] mmCIF format, chain VA [auth E] mmCIF format, chain T [auth A] mmCIF format, chain KB [auth J] mmCIF format, chain DB [auth F]	BC [auth I] DB [auth F] EA [auth C] HC [auth K] KB [auth J] BC [auth I], DB [auth F], EA [auth C], HC [auth K], KB [auth J], NA [auth D], OA [auth D], PB [auth G], S [auth A], T [auth A], UA [auth E], VA [auth E], VB [auth H], WA [auth E], Y [auth B], Z [auth B]	O-(O-(2-AMINOPROPYL)-O'-(2-METHOXYETHYL)POLYPROPYLENE GLYCOL 500) C₃₀ H₆₃ N O₁₀ ICCXIDTYQFYPNV-RUMGZKRTSA-N		Interactions Focus chain BC [auth I] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain HC [auth K] Focus chain KB [auth J] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PB [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain VB [auth H] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain BC [auth I] Focus chain DB [auth F] Focus chain EA [auth C] Focus chain HC [auth K] Focus chain KB [auth J] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PB [auth G] Focus chain S [auth A] Focus chain T [auth A] Focus chain UA [auth E] Focus chain VA [auth E] Focus chain VB [auth H] Focus chain WA [auth E] Focus chain Y [auth B] Focus chain Z [auth B]
A1CIO (Subject of Investigation/LOI) Query on A1CIO Download Ideal Coordinates CCD File SDF format, chain BB [auth F] SDF format, chain DA [auth C] SDF format, chain FC [auth K] SDF format, chain IB [auth J] SDF format, chain KA [auth D] SDF format, chain OB [auth G] SDF format, chain P [auth A] SDF format, chain SA [auth E] SDF format, chain X [auth B] SDF format, chain ZB [auth I] SDF format, chain TB [auth H] SDF format, chain LC [auth L] MOL2 format, chain BB [auth F] MOL2 format, chain DA [auth C] MOL2 format, chain FC [auth K] MOL2 format, chain IB [auth J] MOL2 format, chain KA [auth D] MOL2 format, chain OB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain ZB [auth I] MOL2 format, chain TB [auth H] MOL2 format, chain LC [auth L] mmCIF format, chain BB [auth F] mmCIF format, chain DA [auth C] mmCIF format, chain FC [auth K] mmCIF format, chain IB [auth J] mmCIF format, chain KA [auth D] mmCIF format, chain OB [auth G] mmCIF format, chain P [auth A] mmCIF format, chain SA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain ZB [auth I] mmCIF format, chain TB [auth H] mmCIF format, chain LC [auth L]	BB [auth F] DA [auth C] FC [auth K] IB [auth J] KA [auth D] BB [auth F], DA [auth C], FC [auth K], IB [auth J], KA [auth D], LC [auth L], OB [auth G], P [auth A], SA [auth E], TB [auth H], X [auth B], ZB [auth I]	N-{[4-(4-bromophenyl)-1H-imidazol-2-yl]methyl}-N'-[6-(trifluoromethyl)-1,3-benzothiazol-2-yl]urea C₁₉ H₁₃ Br F₃ N₅ O S OEAUDGBEKDKCMR-UHFFFAOYSA-N		Interactions Focus chain BB [auth F] Focus chain DA [auth C] Focus chain FC [auth K] Focus chain IB [auth J] Focus chain KA [auth D] Focus chain LC [auth L] Focus chain OB [auth G] Focus chain P [auth A] Focus chain SA [auth E] Focus chain TB [auth H] Focus chain X [auth B] Focus chain ZB [auth I] Interactions & Density Focus chain BB [auth F] Focus chain DA [auth C] Focus chain FC [auth K] Focus chain IB [auth J] Focus chain KA [auth D] Focus chain LC [auth L] Focus chain OB [auth G] Focus chain P [auth A] Focus chain SA [auth E] Focus chain TB [auth H] Focus chain X [auth B] Focus chain ZB [auth I]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FB [auth J] SDF format, chain HA [auth D] SDF format, chain IC [auth L] SDF format, chain M [auth A] SDF format, chain PA [auth E] SDF format, chain QB [auth H] SDF format, chain U [auth B] SDF format, chain WB [auth I] SDF format, chain YA [auth F] SDF format, chain LB [auth G] SDF format, chain CC [auth K] MOL2 format, chain AA [auth C] MOL2 format, chain FB [auth J] MOL2 format, chain HA [auth D] MOL2 format, chain IC [auth L] MOL2 format, chain M [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain QB [auth H] MOL2 format, chain U [auth B] MOL2 format, chain WB [auth I] MOL2 format, chain YA [auth F] MOL2 format, chain LB [auth G] MOL2 format, chain CC [auth K] mmCIF format, chain AA [auth C] mmCIF format, chain FB [auth J] mmCIF format, chain HA [auth D] mmCIF format, chain IC [auth L] mmCIF format, chain M [auth A] mmCIF format, chain PA [auth E] mmCIF format, chain QB [auth H] mmCIF format, chain U [auth B] mmCIF format, chain WB [auth I] mmCIF format, chain YA [auth F] mmCIF format, chain LB [auth G] mmCIF format, chain CC [auth K]	AA [auth C] CC [auth K] FB [auth J] HA [auth D] IC [auth L] AA [auth C], CC [auth K], FB [auth J], HA [auth D], IC [auth L], LB [auth G], M [auth A], PA [auth E], QB [auth H], U [auth B], WB [auth I], YA [auth F]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain AA [auth C] Focus chain CC [auth K] Focus chain FB [auth J] Focus chain HA [auth D] Focus chain IC [auth L] Focus chain LB [auth G] Focus chain M [auth A] Focus chain PA [auth E] Focus chain QB [auth H] Focus chain U [auth B] Focus chain WB [auth I] Focus chain YA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain CC [auth K] Focus chain FB [auth J] Focus chain HA [auth D] Focus chain IC [auth L] Focus chain LB [auth G] Focus chain M [auth A] Focus chain PA [auth E] Focus chain QB [auth H] Focus chain U [auth B] Focus chain WB [auth I] Focus chain YA [auth F]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain LA [auth D] MOL2 format, chain LA [auth D] mmCIF format, chain LA [auth D]	LA [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain LA [auth D] Interactions & Density Focus chain LA [auth D]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain CB [auth F] SDF format, chain EB [auth J] SDF format, chain GA [auth C] SDF format, chain GC [auth K] SDF format, chain JB [auth J] SDF format, chain MA [auth D] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain UB [auth H] SDF format, chain XA [auth F] SDF format, chain TA [auth E] SDF format, chain FA [auth C] SDF format, chain AC [auth I] MOL2 format, chain CB [auth F] MOL2 format, chain EB [auth J] MOL2 format, chain GA [auth C] MOL2 format, chain GC [auth K] MOL2 format, chain JB [auth J] MOL2 format, chain MA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain UB [auth H] MOL2 format, chain XA [auth F] MOL2 format, chain TA [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain AC [auth I] mmCIF format, chain CB [auth F] mmCIF format, chain EB [auth J] mmCIF format, chain GA [auth C] mmCIF format, chain GC [auth K] mmCIF format, chain JB [auth J] mmCIF format, chain MA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain UB [auth H] mmCIF format, chain XA [auth F] mmCIF format, chain TA [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain AC [auth I]	AC [auth I] CB [auth F] EB [auth J] FA [auth C] GA [auth C] AC [auth I], CB [auth F], EB [auth J], FA [auth C], GA [auth C], GC [auth K], JB [auth J], MA [auth D], Q [auth A], R [auth A], TA [auth E], UB [auth H], XA [auth F]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain AC [auth I] Focus chain CB [auth F] Focus chain EB [auth J] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain GC [auth K] Focus chain JB [auth J] Focus chain MA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain TA [auth E] Focus chain UB [auth H] Focus chain XA [auth F] Interactions & Density Focus chain AC [auth I] Focus chain CB [auth F] Focus chain EB [auth J] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain GC [auth K] Focus chain JB [auth J] Focus chain MA [auth D] Focus chain Q [auth A] Focus chain R [auth A] Focus chain TA [auth E] Focus chain UB [auth H] Focus chain XA [auth F]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DC [auth K] SDF format, chain GB [auth J] SDF format, chain HB [auth J] SDF format, chain IA [auth D] SDF format, chain JC [auth L] SDF format, chain KC [auth L] SDF format, chain MB [auth G] SDF format, chain N [auth A] SDF format, chain QA [auth E] SDF format, chain RA [auth E] SDF format, chain RB [auth H] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain XB [auth I] SDF format, chain ZA [auth F] SDF format, chain YB [auth I] SDF format, chain SB [auth H] SDF format, chain O [auth A] SDF format, chain NB [auth G] SDF format, chain JA [auth D] SDF format, chain EC [auth K] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DC [auth K] MOL2 format, chain GB [auth J] MOL2 format, chain HB [auth J] MOL2 format, chain IA [auth D] MOL2 format, chain JC [auth L] MOL2 format, chain KC [auth L] MOL2 format, chain MB [auth G] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain RB [auth H] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain XB [auth I] MOL2 format, chain ZA [auth F] MOL2 format, chain YB [auth I] MOL2 format, chain SB [auth H] MOL2 format, chain O [auth A] MOL2 format, chain NB [auth G] MOL2 format, chain JA [auth D] MOL2 format, chain EC [auth K] mmCIF format, chain AB [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DC [auth K] mmCIF format, chain GB [auth J] mmCIF format, chain HB [auth J] mmCIF format, chain IA [auth D] mmCIF format, chain JC [auth L] mmCIF format, chain KC [auth L] mmCIF format, chain MB [auth G] mmCIF format, chain N [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain RB [auth H] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain XB [auth I] mmCIF format, chain ZA [auth F] mmCIF format, chain YB [auth I] mmCIF format, chain SB [auth H] mmCIF format, chain O [auth A] mmCIF format, chain NB [auth G] mmCIF format, chain JA [auth D] mmCIF format, chain EC [auth K]	AB [auth F] BA [auth C] CA [auth C] DC [auth K] EC [auth K] AB [auth F], BA [auth C], CA [auth C], DC [auth K], EC [auth K], GB [auth J], HB [auth J], IA [auth D], JA [auth D], JC [auth L], KC [auth L], MB [auth G], N [auth A], NB [auth G], O [auth A], QA [auth E], RA [auth E], RB [auth H], SB [auth H], V [auth B], W [auth B], XB [auth I], YB [auth I], ZA [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DC [auth K] Focus chain EC [auth K] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain JC [auth L] Focus chain KC [auth L] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NB [auth G] Focus chain O [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain SB [auth H] Focus chain V [auth B] Focus chain W [auth B] Focus chain XB [auth I] Focus chain YB [auth I] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DC [auth K] Focus chain EC [auth K] Focus chain GB [auth J] Focus chain HB [auth J] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain JC [auth L] Focus chain KC [auth L] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NB [auth G] Focus chain O [auth A] Focus chain QA [auth E] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain SB [auth H] Focus chain V [auth B] Focus chain W [auth B] Focus chain XB [auth I] Focus chain YB [auth I] Focus chain ZA [auth F]