SAXSdb — 8d1u

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1. Protein Identity and Related Structures Protein Identity & Related Structures

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

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–317	Non-standard monomer：Yes (specific site not provided by mmCIF)	UT7 oxa(dethia)-CoA × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；75 mM Magnesium Chloride, 20% PEG 6000, 3% PEG 400	Resolution 1.30 Å R-free 0.167

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8D1U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EBL THE 1.8 A CRYSTAL STRUCTURE AND ACTIVE SITE ARCHITECTURE OF BETA-KETOACYL-[ACYL CARRIER PROTEIN] SYNTHASE III (FABH) FROM ESCHERICHIA COLI Deposited 2000-01-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.8-2.0 M ammonium sulphate, 2% PEG 400, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.225
1HN9 CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III Deposited 2000-12-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEK4000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.00 Å R-free 0.218
1HND CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III-COA COMPLEX Deposited 2000-12-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa）	Not recorded	COA COENZYME A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.257
1HNH CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III + DEGRADED FORM OF ACETYL-COA Deposited 2000-12-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEK4000, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.90 Å R-free 0.274
1HNJ CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III + MALONYL-COA Deposited 2000-12-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa）	Not recorded	PO4 PHOSPHATE ION × 2 MLC MALONYL-COENZYME A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.46 Å R-free 0.193
1HNK CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III, APO TETRAGONAL FORM Deposited 2000-12-07	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.240
1MZS CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III WITH BOUND dichlorobenzyloxy-indole-carboxylic acid inhibitor Deposited 2002-10-09	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–317（317 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1 669 1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；278 K；20% PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K	Resolution 2.10 Å R-free 0.230
1MZS CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III WITH BOUND dichlorobenzyloxy-indole-carboxylic acid inhibitor Deposited 2002-10-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2 669 1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；278 K；20% PEG 8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K	Resolution 2.10 Å R-free 0.230
2EFT Methanethiol-CYS 112 inhibition complex of E. coli ketoacyl synthase III (FABH) and Coenzyme A (high concentration (1.7mM) soak) Deposited 2007-02-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Not recorded	SO4 SULFATE ION × 2 COA COENZYME A × 1 MEE METHANETHIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.7M AMMONIUM SULFATE, 2% PEG 400, 100MM NA HEPES, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.246
2GYO Methanethiol-Cys 112 Inhibition Complex of E. Coli Ketoacyl Synthase III (FabH) and Coenzyme A Deposited 2006-05-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Not recorded	COA COENZYME A × 1 MEE METHANETHIOL × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；1.7M ammonium sulfate, 2% PEG400, 100 mM Na Hepes (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.268
3IL9 Structure of E. coli FabH Deposited 2009-08-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；12% PEG 3350, 5 mM calcium acetate, 0.1 M HEPES, pH 7.5, 2 mM TCEP and 1% DMSO, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 1.85 Å R-free 0.213
5BNM E. coli FabH with Small Molecule Inhibitor 1 Deposited 2015-05-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Not recorded	SO4 SULFATE ION × 1 4VK N-{[3'-(hydroxymethyl)biphenyl-4-yl]methyl}benzenesulfonamide × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；14% PEG 4000, 0.1 M magnesium chloride, 0.1 M Tris	Resolution 1.70 Å R-free 0.269
5BNR E. coli Fabh with small molecule inhibitor 2 Deposited 2015-05-26	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa）	Not recorded	4VL 1-{5-[2-fluoro-5-(hydroxymethyl)phenyl]pyridin-2-yl}piperidine-4-carboxylic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；14% PEG 4000, magnesium chloride, 0.1 M Tris	Resolution 1.89 Å R-free 0.245
5BNS E. coli Fabh with small molecule inhibitor 2 Deposited 2015-05-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Not recorded	4VM 1-{5-[2-fluoro-5-(hydroxymethyl)phenyl]pyridin-2-yl}-N-(quinolin-6-ylmethyl)piperidine-4-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；14% PEG 4000, 0.1 M magnesium chloride, 0.1 m Tris	Resolution 2.20 Å R-free 0.287
6X7R E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) in complex with oxa(dethia)-coenzyme A Deposited 2020-05-30	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa）	Not recorded	UT7 oxa(dethia)-CoA × 2 MG MAGNESIUM ION × 2 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；75 mM magnesium chloride, 100 mM HEPES:NaOH, pH 7.5, 23% PEG3350, 1.5% DMSO	Resolution 1.35 Å R-free 0.176
9KA2 Crystal structure of beta-ketoacyl-ACP synthase FabH from E. coli Deposited 2024-10-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris Bicine, PH8.5, 10% w/v PEG 20000	Resolution 1.50 Å R-free 0.198
9KA5 Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q from E. coli Deposited 2024-10-28	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–317（317 aa）	Mutation：C112Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Tris Bicine, PH8.5, 10% w/v PEG 20000	Resolution 1.42 Å R-free 0.192
9KA6 Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q in complex with acyl-ACP from E. coli Deposited 2024-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Mutation：C112Q Mutation：C112Q	6VG ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] ethanethioate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.0M sodium chloride,0.1M HEPES PH7.0	Resolution 1.47 Å R-free 0.178
9KA7 Crystal structure of beta-ketoacyl-ACP synthase FabH C112Q in complex with malonyl-ACP from E. coli Deposited 2024-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–317（317 aa） Chain B 1–317（317 aa）	Mutation：C112Q Mutation：C112Q	A1EE0 3-[2-[3-[[(2R)-4-bis(oxidanyl)phosphanyloxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]-3-oxidanylidene-propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.0M sodium chloride,0.1M HEPES PH7.0	Resolution 2.30 Å R-free 0.207

18 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FABH_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–320； UniProt 1–317

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8d1u
Deposition date deposition_date	2022-05-27
Structure title title	E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) with an acetylated cysteine and in complex with oxa(dethia)-Coenzyme A
Keywords keywords	Ketoacyl synthase, substrate analog, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.15 Å
Radius of gyration Rg (electron density) rg_electron	18.91 Å
Forward intensity I(0) i0	21648100.00
Molecular weight molecular_weight	34390.0 kDa
Excluded volume excluded_volume	42637 Å³
Envelope volume envelope_volume	48833 Å³
Hydration-shell volume shell_volume	21146 Å³
Envelope diameter envelope_diameter	63.6 Å
Shell Rg shell_rg	25.81 Å
Envelope Rg envelope_rg	19.31 Å
Shape Rg shape_rg	18.90 Å
Total Rg total_rg	19.85 Å
Total atoms total_atoms	2407
Residues n_residues	317
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	63.0 Å
Rg (real space) rg_real	20.04 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	2.1650e+07
I(0) uncertainty (real space) i0_real_error	2.7310e+05
Rg (reciprocal space) rg_reciprocal	20.06 Å
I(0) (reciprocal space) i0_reciprocal	21650000.0000
Solution quality estimate total_estimate	0.8991
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.1 Å
Skewness Skewness skewness	0.188
Kurtosis Kurtosis kurtosis	-0.392
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4113000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	3-oxoacyl-[acyl-carrier-protein] synthase 3
Molecular weight formula_weight	33790.2 kDa
EC 编号 ec_number	2.3.1.180
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3081

SGGMYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFEAATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDVAAACAGFTYALSVADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDGAGAAVLAASEEPGIISTHLHADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQLDWLVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASVPCALDEAVRDGRIKPGQLVLLEAFGGGFTWGSALVRF

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	oxa(dethia)-CoA
Molecular weight formula_weight	751.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	506

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8. Citations (1)

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Unit-cell length a length_a	72.662 Å
Unit-cell length b length_b	72.662 Å
Unit-cell length c length_c	102.852 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.302 Å
Low-resolution limit resolution_low	22.992 Å
R factor r_factor	—
R_work r_work	0.1427
R_free r_free	0.1668

fit	/app/data/saxs_computation/d1/8d1u/8d1u.fit
pddf	/app/data/pr_computation/d1/8d1u/8d1u.pr.out
profile	/app/data/saxs_computation/d1/8d1u/8d1u.dat

E. coli beta-ketoacyl-[acyl carrier protein] synthase III (FabH) with an acetylated cysteine and in complex with oxa(dethia)-Coenzyme A

1. Protein Identity and Related Structures Protein Identity & Related Structures

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

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction