8PD1

Pseudomonas aeruginosa FabF C164A mutant in complex with N-isopropyl-1H-imidazole-4-carboxamide

PDB DOI: https://doi.org/10.2210/pdb8PD1/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-06-11 Released: 2024-01-10
Deposition Author(s): Georgiou, C., Brenk, R., Yadrykhinsky, V., Espeland, L.O.
Funding Organization(s): Research Council of Norway

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.196
R-Value Work: 0.158
R-Value Observed: 0.159

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

New starting points for antibiotics targeting P. aeruginosa FabF discovered by crystallographic fragment screening followed by hit expansion

Georgiou, C., Espeland, L.O., Bukya, H., Yadrykhinsky, V., Haug, B.E., Mainkar, P., Brenk, R.

(2023) ChemRxiv

DOI: https://doi.org/10.26434/chemrxiv-2023-cwk25

Macromolecule Content

Total Structure Weight: 89.75 kDa
Atom Count: 6,447
Modelled Residue Count: 821
Deposited Residue Count: 838
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] synthase 2	A, B	419	Pseudomonas aeruginosa	Mutation(s): 1 Gene Names: fabF1, PA2965 EC: 2.3.1.179
UniProt
Find proteins for G3XDA2 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore G3XDA2 Go to UniProtKB: G3XDA2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G3XDA2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YHU (Subject of Investigation/LOI) Query on YHU Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain O [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain O [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain O [auth A]	AA [auth B], O [auth A]	~{N}-propan-2-yl-1~{H}-imidazole-4-carboxamide C₇ H₁₁ N₃ O OWYKHVLWBVIMNI-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain O [auth A] Interactions & Density Focus chain AA [auth B] Focus chain O [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain K [auth A] mmCIF format, chain E [auth A] mmCIF format, chain K [auth A]	E [auth A], K [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain K [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain P [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	C [auth A] D [auth A] F [auth A] H [auth A] I [auth A] C [auth A], D [auth A], F [auth A], H [auth A], I [auth A], P [auth B], V [auth B], W [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain V [auth B] Focus chain W [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	G [auth A] J [auth A] L [auth A] M [auth A] N [auth A] G [auth A], J [auth A], L [auth A], M [auth A], N [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], X [auth B], Y [auth B], Z [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]