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2c9h

Structure of mitochondrial beta-ketoacyl synthase

Method: X-RAY DIFFRACTION Dmax: 71.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

MITOCHONDRIAL BETA-KETOACYL SYNTHASE

HOMO SAPIENS

UniProt Q9NWU1

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 39–459 Non-standard monomer：Yes (specific site not provided by mmCIF) NI NICKEL (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；0.1 M BIS-TRIS PH=5.5, 25% PEG3350, 0.20 M NH4AC, pH 5.50 Resolution 1.80 Å R-free 0.240

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 2C9H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2IWY Human mitochondrial beta-ketoacyl ACP synthase Deposited 2006-07-05 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 38–459（422 aa） Fragment：RESIDUES 38-459
Chain B 38–459（422 aa） Fragment：RESIDUES 38-459
Not recorded NH4 AMMONIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；24% PEG-3350, 0.2 M NH4CL, pH 7.80
Resolution 2.06 Å R-free 0.205
2IWZ Human mitochondrial beta-ketoacyl ACP synthase complexed with hexanoic acid Deposited 2006-07-05 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 38–459（422 aa） Fragment：RESIDUES 38-459
Chain B 38–459（422 aa） Fragment：RESIDUES 38-459
Not recorded 6NA HEXANOIC ACID × 2 NH4 AMMONIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；24% PEG3350, 0.2M NH4CL, pH 7.80
Resolution 1.65 Å R-free 0.188
9N50 Crosslinked Crystal Structure of Human Mitochondrial Ketosynthase, OXSM, and Crosslinker-crypto Human Mitochondrial Acyl Carrier Protein, C8aBr-mACP Deposited 2025-02-03 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 38–459（422 aa） Fragment：residues 38-459
Chain B 38–459（422 aa） Fragment：residues 38-459
Not recorded A1BMZ N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-octanamidoethyl)-beta-alaninamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.5 M ammonium sulfate, 1 M lithium sulfate, and 0.1 M sodium citrate pH 5.6
Resolution 2.50 Å
9N51 Crosslinked Crystal Structure of Human Mitochondrial Ketosynthase, OXSM, and Crosslinker-crypto Human Mitochondrial Acyl Carrier Protein, C8Cl-mACP Deposited 2025-02-03 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 38–459（422 aa） Fragment：residues 38-459
Chain B 38–459（422 aa） Fragment：residues 38-459
Not recorded A1BMZ N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-octanamidoethyl)-beta-alaninamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.5 M ammonium sulfate, 1 M lithium sulfate, and 0.1 M sodium citrate pH 5.6
Resolution 2.31 Å R-free 0.273
9N51 Crosslinked Crystal Structure of Human Mitochondrial Ketosynthase, OXSM, and Crosslinker-crypto Human Mitochondrial Acyl Carrier Protein, C8Cl-mACP Deposited 2025-02-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 38–459（422 aa） Fragment：residues 38-459
Chain E 38–459（422 aa） Fragment：residues 38-459
Not recorded A1BMZ N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-N-(2-octanamidoethyl)-beta-alaninamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.5 M ammonium sulfate, 1 M lithium sulfate, and 0.1 M sodium citrate pH 5.6
Resolution 2.31 Å R-free 0.273

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9NWU1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 24–444； UniProt 39–459

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 2c9h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2c9h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2c9h
Deposition date deposition_date2005-12-12
Structure title titleStructure of mitochondrial beta-ketoacyl synthase
Keywords keywordsTRANSFERASE, FATTY ACID SYNTHESIS, MITOCHONDRIA, KETOACYL SYNTHASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.80 Å
Radius of gyration Rg (electron density) rg_electron20.81 Å
Forward intensity I(0) i033692500.00
Molecular weight molecular_weight44236.0 kDa
Excluded volume excluded_volume55104 ų
Envelope volume envelope_volume63798 ų
Hydration-shell volume shell_volume24883 ų
Envelope diameter envelope_diameter73.8 Å
Shell Rg shell_rg28.35 Å
Envelope Rg envelope_rg21.48 Å
Shape Rg shape_rg20.84 Å
Total Rg total_rg21.65 Å
Total atoms total_atoms3108
Residues n_residues426
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax71.4 Å
Rg (real space) rg_real21.70 Å
Rg uncertainty (real space) rg_real_error0.35 Å
I(0) (real space) i0_real3.3690e+07
I(0) uncertainty (real space) i0_real_error4.5990e+05
Rg (reciprocal space) rg_reciprocal21.72 Å
I(0) (reciprocal space) i0_reciprocal33690000.0000
Solution quality estimate total_estimate0.8837
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.6 Å
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.282
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7487000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.987
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2c9ha1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.0 — automated matches
Domain ID domain_idd2c9ha2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.95 — Thiolase-like
Superfamily Superfamily superfamilyc.95.1 — Thiolase-like
Family Family familyc.95.1.0 — automated matches
Domain ID domain_idd2c9ha3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id2c9hA01
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_id2c9hA02
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
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8. Citations (1)

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9. Files and Curves (10)