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1buc

THREE-DIMENSIONAL STRUCTURE OF BUTYRYL-COA DEHYDROGENASE FROM MEGASPHAERA ELSDENII

Method: X-RAY DIFFRACTION Dmax: 107.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BUTYRYL-COA DEHYDROGENASE

Megasphaera elsdenii

UniProt Q06319

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–383 Chain B； UniProt 1–383 Not recorded CAA ACETOACETYL-COENZYME A × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.50 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name ACDS_MEGEL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–383； UniProt 1–383 Author chain B； PDBConstruct 1–383； UniProt 1–383

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 1buc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1buc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1buc
Deposition date deposition_date1994-09-06
Structure title titleTHREE-DIMENSIONAL STRUCTURE OF BUTYRYL-COA DEHYDROGENASE FROM MEGASPHAERA ELSDENII
Keywords keywordsACYL-COA DEHYDROGENASE SHORT-CHAIN ACYL-COA DEHYDROGENASE, FLAVOPROTEIN, OXIDOREDUCTASE; OXIDOREDUCTASE
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_guinier30.12 Å
Radius of gyration Rg (electron density) rg_electron29.51 Å
Forward intensity I(0) i0120853000.00
Molecular weight molecular_weight86067.0 kDa
Excluded volume excluded_volume107220 ų
Envelope volume envelope_volume126330 ų
Hydration-shell volume shell_volume35964 ų
Envelope diameter envelope_diameter115.3 Å
Shell Rg shell_rg36.34 Å
Envelope Rg envelope_rg29.65 Å
Shape Rg shape_rg29.54 Å
Total Rg total_rg30.00 Å
Total atoms total_atoms6032
Residues n_residues766
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 dmax107.0 Å
Rg (real space) rg_real30.19 Å
Rg uncertainty (real space) rg_real_error1.16 Å
I(0) (real space) i0_real1.2090e+08
I(0) uncertainty (real space) i0_real_error2.1330e+06
Rg (reciprocal space) rg_reciprocal30.16 Å
I(0) (reciprocal space) i0_reciprocal120800000.0000
Solution quality estimate total_estimate0.8557
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.3 Å
Skewness Skewness skewness0.439
Kurtosis Kurtosis kurtosis-0.213
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29030000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.737; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; 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) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1buca1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family familya.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
Domain ID domain_idd1buca2
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamilye.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family familye.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains
Domain ID domain_idd1bucb1
Class classa — All alpha proteins
Fold Fold folda.29 — Bromodomain-like
Superfamily Superfamily superfamilya.29.3 — Acyl-CoA dehydrogenase C-terminal domain-like
Family Family familya.29.3.1 — Medium chain acyl-CoA dehydrogenase-like, C-terminal domain
Domain ID domain_idd1bucb2
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.6 — Acyl-CoA dehydrogenase NM domain-like
Superfamily Superfamily superfamilye.6.1 — Acyl-CoA dehydrogenase NM domain-like
Family Family familye.6.1.1 — Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains

CATH v4.4 (6 domains)

Domain ID domain_id1bucA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain
Domain ID domain_id1bucA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2
Domain ID domain_id1bucA03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
Domain ID domain_id1bucB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology540 — Butyryl-Coa Dehydrogenase, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acyl-CoA dehydrogenase/oxidase, N-terminal domain
Domain ID domain_id1bucB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology110 — Butyryl-CoA Dehydrogenase, subunit A; domain 2
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 2
Domain ID domain_id1bucB03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3
Homologous superfamily homologous superfamily10 — Butyryl-CoA Dehydrogenase, subunit A, domain 3
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8. Citations (1)

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9. Files and Curves (10)