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2p8u

Crystal structure of human 3-hydroxy-3-methylglutaryl CoA synthase I

Method: X-RAY DIFFRACTION Dmax: 92.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hydroxymethylglutaryl-CoA synthase, cytoplasmic

Homo sapiens

UniProt Q01581

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 16–470 Chain B； UniProt 16–470 Non-standard monomer：Yes (specific site not provided by mmCIF) COA COENZYME A × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；0.2M (NH4)2SO4, 0.1M Bis-Tris pH 6.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K Resolution 2.00 Å R-free 0.202

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 2P8U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9ZAW HMG-CoA synthase 1 (HMGCS1) bound to inhibitor compound CNP7 Deposited 2025-11-19 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 16–470（455 aa）
Chain B 16–470（455 aa）
Not recorded A1C1C (3S)-1-[(Z)-iminomethyl]-N-({(1P)-3'-[(prop-2-yn-1-yl)carbamoyl][1,1'-biphenyl]-3-yl}methyl)pyrrolidine-3-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.29 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HMCS1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 24–478； UniProt 16–470 Author chain B； PDBConstruct 24–478； UniProt 16–470

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 2p8u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2p8u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2p8u
Deposition date deposition_date2007-03-23
Structure title titleCrystal structure of human 3-hydroxy-3-methylglutaryl CoA synthase I
Keywords keywordshydromethylglutaryl CoA, mevalonate pathway, Structural Genomics, Structural Genomics Consortium, SGC, TRANSFERASE; 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_guinier28.75 Å
Radius of gyration Rg (electron density) rg_electron27.60 Å
Forward intensity I(0) i0175721000.00
Molecular weight molecular_weight103080.0 kDa
Excluded volume excluded_volume127860 ų
Envelope volume envelope_volume148520 ų
Hydration-shell volume shell_volume42735 ų
Envelope diameter envelope_diameter97.8 Å
Shell Rg shell_rg36.77 Å
Envelope Rg envelope_rg27.99 Å
Shape Rg shape_rg27.62 Å
Total Rg total_rg28.31 Å
Total atoms total_atoms7237
Residues n_residues922
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 dmax92.8 Å
Rg (real space) rg_real28.64 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real1.7570e+08
I(0) uncertainty (real space) i0_real_error2.7860e+06
Rg (reciprocal space) rg_reciprocal28.69 Å
I(0) (reciprocal space) i0_reciprocal175700000.0000
Solution quality estimate total_estimate0.8874
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.4 Å
Skewness Skewness skewness0.259
Kurtosis Kurtosis kurtosis-0.330
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha54820000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.858; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.958
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id2p8uA00
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_id2p8uB00
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)