7L00 | pdb_00007l00

Crystal Structure of C. difficile Enoyl-Acyl Carrier Protein Reductase (FabK) in Complex with an Inhibitor

PDB DOI: https://doi.org/10.2210/pdb7L00/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Clostridioides difficile
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2020-12-10 Released: 2021-12-22
Deposition Author(s): Akhtar, A., Santarsiero, B.D., Hevener, K.E.
Funding Organization(s): Department of Defense (DOD, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.185 (Depositor), 0.187 (DCC)
R-Value Work:
0.144 (Depositor), 0.146 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of C. difficile Enoyl-Acyl Carrier Protein Reductase (FabK) in Complex with an Inhibitor

Jones, J.A., Hevener, K.E., Alghanim, L., Akhtar, A., Santarsiero, B.D.

To be published.

Macromolecule Content

Total Structure Weight: 136.67 kDa
Atom Count: 10,220
Modeled Residue Count: 1,251
Deposited Residue Count: 1,260
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-Acyl Carrier Protein Reductase FabK	A, B, C, D	315	Clostridioides difficile	Mutation(s): 0 Gene Names: fabK, BN1095_450087, BN1096_560086, BN1097_540088, cdgr_10495, E5F33_11835, E5F39_12870, E5F43_13130, FQN08_05765, SAMEA1402373_02260... fabK, BN1095_450087, BN1096_560086, BN1097_540088, cdgr_10495, E5F33_11835, E5F39_12870, E5F43_13130, FQN08_05765, SAMEA1402373_02260, SAMEA1402406_01811, SAMEA1402410_02165, SAMEA1710795_00230, SAMEA2239407_02705, SAMEA3374989_02524, SAMEA3375037_01248, SAMEA3375041_00754, SAMEA708418_02261 EC: 1.3.1.9 (PDB Primary Data), 1.13.12.16 (PDB Primary Data)
UniProt
Find proteins for A0A031WIF2 (Clostridioides difficile) Explore A0A031WIF2 Go to UniProtKB: A0A031WIF2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A031WIF2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth D]	E [auth A], J [auth B], N [auth C], S [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain S [auth D]
XCJ (Subject of Investigation/LOI) Query on XCJ Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain F [auth A]	F [auth A], K [auth B], O [auth C], T [auth D]	N-[6-(methylsulfonyl)-1,3-benzothiazol-2-yl]-2-[2-(1H-pyrrol-1-yl)-1,3-thiazol-4-yl]acetamide C₁₇ H₁₄ N₄ O₃ S₃ KRKFVNMZGZWPHC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain T [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain I [auth A] MOL2 format, chain R [auth C] MOL2 format, chain I [auth A] mmCIF format, chain R [auth C] mmCIF format, chain I [auth A]	I [auth A], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain R [auth C] Interactions & Density Focus chain I [auth A] Focus chain R [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain M [auth B]	G [auth A] H [auth A] L [auth B] M [auth B] P [auth C] G [auth A], H [auth A], L [auth B], M [auth B], P [auth C], Q [auth C], U [auth D], V [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D]