5bnm

E. coli FabH with Small Molecule Inhibitor 1

Method: X-RAY DIFFRACTION Dmax: 80.4 Å Quality: GOOD

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

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

Escherichia coli

UniProt P0A6R0

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 Chain B; UniProt 1–317 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

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.

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 1–317; UniProt 1–317 Author chain B; PDBConstruct 1–317; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 5bnm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5bnm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5bnm
Deposition date deposition_date2015-05-26
Structure title titleE. coli FabH with Small Molecule Inhibitor 1
Keywords keywordsFabH, Fatty Acid Synthesis, Bacterial Enzyme, Transferase-Transferase Inhibitor complex; Transferase/Transferase Inhibitor
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.16
Radius of gyration Rg (electron density) rg_electron23.98
Forward intensity I(0) i076520300.00
Molecular weight molecular_weight67650.0 kDa
Excluded volume excluded_volume84355 ų
Envelope volume envelope_volume96716 ų
Hydration-shell volume shell_volume32453 ų
Envelope diameter envelope_diameter83.0
Shell Rg shell_rg32.36
Envelope Rg envelope_rg24.34
Shape Rg shape_rg23.96
Total Rg total_rg24.89
Total atoms total_atoms4745
Residues n_residues634
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax80.4
Rg (real space) rg_real25.07
Rg uncertainty (real space) rg_real_error0.46
I(0) (real space) i0_real7.6520e+07
I(0) uncertainty (real space) i0_real_error1.0590e+06
Rg (reciprocal space) rg_reciprocal25.10
I(0) (reciprocal space) i0_reciprocal76520000.0000
Solution quality estimate total_estimate0.8934
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.6
Skewness Skewness skewness0.289
Kurtosis Kurtosis kurtosis-0.311
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22750000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5bnma1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like
Domain ID domain_idd5bnma2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like
Domain ID domain_idd5bnmb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like
Domain ID domain_idd5bnmb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.2 — Chalcone synthase-like

CATH v4.4 (4 domains)

Domain ID domain_id5bnmA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id5bnmA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id5bnmB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase
Domain ID domain_id5bnmB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology47 — Peroxisomal Thiolase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Thiolase/Chalcone synthase

8. Citations (1)

9. Files and Curves (10)