PDB-9gqv: Pseudomonas aeruginosa FabF C164A in complex with N-((1-((2-hydro...

ID or keywords:

Entry

Database: PDB / ID: 9gqv

Title

Pseudomonas aeruginosa FabF C164A in complex with N-((1-((2-hydroxy-4-methylpentanamido)methyl)cyclobutyl)methyl)-1H-pyrazole-3-carboxamide

Components

3-oxoacyl-[acyl-carrier-protein] synthase 2

Keywords

TRANSFERASE / inhibitor / protein-ligand complex / FabF

Function / homology

Function and homology information

beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.766 Å

Authors

Yadrykhins'ky, V. / Brenk, R.

Funding support

Norway, 2items

Citation

Journal: Eur.J.Med.Chem. / Year: 2025
Title: Towards new antibiotics: P. aeruginosa FabF ligands discovered by crystallographic fragment screening followed by hit expansion.
Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhins'ky, V. / Haug, B.E. / Mainkar, P.S. / Brenk, R.

History

Deposition	Sep 9, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 7, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9gqv.cif.gz	732.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	9gqv_validation.pdf.gz	939.3 KB	Display	wwPDB validaton report
Full document	9gqv_full_validation.pdf.gz	939.6 KB	Display
Data in XML	9gqv_validation.xml.gz	39.4 KB	Display
Data in CIF	9gqv_validation.cif.gz	53.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gq/9gqv ftp://data.pdbj.org/pub/pdb/validation_reports/gq/9gqv	HTTPS FTP

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Related structure data

Related structure data	5sn5C 5sn6C 5sn7C 5sn8C 5sn9C 5snaC 5snbC 5sncC 5sndC 5sneC 5snfC 5sngC 5snhC 5sniC 5snjC 5snkC 5snlC 5snmC 5snnC 5snoC 5snpC 5snqC 5snrC 5snsC 5sntC 5snuC 5snvC 5snwC 5snxC 5snyC 5snzC 5so0C 5so1C 5so2C 5so3C 5so4C 5so5C 5so6C 5so7C 5so8C 5so9C 5soaC 5sobC 5socC 5sodC 5soeC 5sofC 5sogC 5sohC 8cn2C 8cn4C 8cn5C 8cn7C 8cn8C 8cneC 8cngC 8couC 8covC 8pd1C 8pfzC 8qerC 8qm1C 9i76C 9i7kC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

Similar structure data

Similarity search - Function & homology

F&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (12) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: 3-oxoacyl-[acyl-carrier-protein] synthase 2

B: 3-oxoacyl-[acyl-carrier-protein] synthase 2

hetero molecules

90 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 3-oxoacyl-[acyl-carrier-protein] synthase 2

hetero molecules

defined by author
Evidence: From the literature review: A dimer is suggested via analysis of the apo structure using PISA (Baum et al., 2015)
45 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 3-oxoacyl-[acyl-carrier-protein] synthase 2

hetero molecules

defined by author
45 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.679, 103.811, 143.318
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 413 / Label seq-ID: 9 - 418

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein , 1 types, 2 molecules AB

#1: Protein	3-oxoacyl-[acyl-carrier-protein] synthase 2 Mass: 43996.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fabF1, PA2965 / Production host: Escherichia coli (E. coli) References: UniProt: G3XDA2, beta-ketoacyl-[acyl-carrier-protein] synthase II

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Non-polymers , 5 types, 371 molecules

#2: Chemical	ChemComp-A1IOR / ~{N}-[[1-[[[(2~{S})-4-methyl-2-oxidanyl-pentanoyl]amino]methyl]cyclobutyl]methyl]-1~{H}-pyrazole-3-carboxamide Mass: 322.403 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₂₆N₄O₃ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.45 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.24M ammonium formate and 35% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8731 Å / Relative weight: 1
Reflection	Resolution: 1.766→51.91 Å / Num. obs: 73113 / % possible obs: 99.21 % / Redundancy: 4.6 % / CC_1/2: 0.989 / R_merge(I) obs: 0.099 / R_pim(I) all: 0.053 / R_rim(I) all: 0.113 / Net I/av σ(I): 10 / Net I/σ(I): 8.1
Reflection shell	Resolution: 1.77→1.8 Å / Redundancy: 4.3 % / R_merge(I) obs: 1.276 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3398 / CC_1/2: 0.28 / R_pim(I) all: 0.713 / R_rim(I) all: 1.471 / % possible all: 93.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
xia2	3.12.0	data reduction
DIALS	3.12.1	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.766→51.905 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.942 / SU B: 8.159 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.128 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2222	3737	5.113 %
R_work	0.1818	69350	-
all	0.184	-	-
obs	-	73087	99.151 %

Solvent computation

Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 33.684 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.689 Å²	-0 Å²	-0 Å²
2-	-	1.325 Å²	-0 Å²
3-	-	-	-0.637 Å²

Refinement step

Cycle: LAST / Resolution: 1.766→51.905 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6032	0	124	345	6501

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	6308
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.016	5956
X-RAY DIFFRACTION	r_angle_refined_deg	1.976	1.804	8521
X-RAY DIFFRACTION	r_angle_other_deg	1.035	1.737	13644
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.371	5	844
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.27	5.938	64
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.787	5	4
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.066	10	964
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.772	10	263
X-RAY DIFFRACTION	r_chiral_restr	0.114	0.2	943
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	7737
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	1493
X-RAY DIFFRACTION	r_nbd_refined	0.179	0.2	1149
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.145	0.2	5458
X-RAY DIFFRACTION	r_nbtor_refined	0.147	0.2	3031
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.066	0.2	3313
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.107	0.2	382
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.055	0.2	20
X-RAY DIFFRACTION	r_nbd_other	0.114	0.2	236
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.101	0.2	31
X-RAY DIFFRACTION	r_mcbond_it	2.708	2.342	3310
X-RAY DIFFRACTION	r_mcbond_other	2.707	2.343	3311
X-RAY DIFFRACTION	r_mcangle_it	3.385	4.217	4143
X-RAY DIFFRACTION	r_mcangle_other	3.385	4.219	4144
X-RAY DIFFRACTION	r_scbond_it	4.114	2.902	2998
X-RAY DIFFRACTION	r_scbond_other	4.114	2.903	2999
X-RAY DIFFRACTION	r_scangle_it	5.838	5.104	4363
X-RAY DIFFRACTION	r_scangle_other	5.838	5.104	4364
X-RAY DIFFRACTION	r_lrange_it	6.905	24.146	6771
X-RAY DIFFRACTION	r_lrange_other	6.862	24.026	6711
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.056	0.05	13040

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.05636	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.05636	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.766-1.812	0.342	236	0.331	4878	0.332	5372	0.902	0.904	95.1973	0.321
1.812-1.861	0.298	289	0.305	4981	0.305	5281	0.921	0.921	99.7917	0.289
1.861-1.915	0.279	284	0.277	4793	0.277	5078	0.94	0.942	99.9803	0.253
1.915-1.974	0.238	234	0.248	4737	0.248	4972	0.958	0.956	99.9799	0.219
1.974-2.039	0.241	232	0.228	4589	0.228	4825	0.958	0.964	99.9171	0.19
2.039-2.11	0.253	263	0.212	4413	0.214	4677	0.957	0.969	99.9786	0.171
2.11-2.19	0.234	258	0.187	4274	0.19	4536	0.965	0.977	99.9118	0.15
2.19-2.279	0.229	230	0.176	4089	0.179	4323	0.963	0.98	99.9075	0.136
2.279-2.38	0.203	195	0.17	3949	0.172	4157	0.974	0.982	99.6873	0.132
2.38-2.496	0.242	197	0.168	3790	0.172	4012	0.959	0.983	99.3769	0.131
2.496-2.631	0.203	209	0.164	3468	0.167	3782	0.975	0.984	97.2237	0.131
2.631-2.79	0.194	173	0.154	3439	0.156	3631	0.977	0.986	99.4767	0.122
2.79-2.982	0.189	139	0.151	3240	0.152	3382	0.976	0.986	99.9113	0.124
2.982-3.22	0.242	147	0.174	2998	0.177	3152	0.963	0.98	99.7779	0.149
3.22-3.526	0.188	151	0.152	2767	0.154	2931	0.979	0.986	99.5565	0.136
3.526-3.939	0.212	125	0.163	2517	0.165	2656	0.975	0.985	99.4729	0.152
3.939-4.545	0.175	145	0.149	2219	0.15	2384	0.981	0.986	99.1611	0.145
4.545-5.555	0.209	98	0.168	1865	0.17	2012	0.977	0.984	97.5646	0.165
5.555-7.812	0.227	76	0.2	1475	0.201	1580	0.964	0.974	98.1646	0.192
7.812-51.905	0.306	56	0.217	869	0.223	948	0.917	0.956	97.5738	0.225

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.0057	-0.0518	-0.499	0.0047	0.0212	0.2588	-0.0399	-0.0988	0.0346	-0.0019	0.0129	-0.0172	0.0353	0.0567	0.027	0.0149	0.0172	0.0269	0.0481	-0.0071	0.1364	-35.8904	-3.6124	32.249
2	0.2012	0.0819	0.0728	0.3711	0.2651	0.2163	-0.0046	0.0078	-0.0711	0.0313	0.018	-0.0381	0.0182	-0.0157	-0.0135	0.0211	0.0002	0.0064	0.0349	0.0083	0.1404	-5.2089	-14.2514	68.2456

Refinement TLS group

Selection: ALL

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