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1b16

ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLEX WITH NAD-3-PENTANONE

Method: X-RAY DIFFRACTION Dmax: 82.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (ALCOHOL DEHYDROGENASE)

OrganismNot specified

UniProt P10807

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 1–254 Chain B； UniProt 1–254 Not recorded NAQ NICOTINAMIDE ADENINE DINUCLEOTIDE 3-PENTANONE ADDUCT × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 28% PEG 2000, 0.2 M CACL2, 0.1 M TRIS-HCL, PH= 7.5, 1MM NAD+, 1% 3-PENTANONE, 4 C. Resolution 1.40 Å R-free 0.213

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 1B16 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A4U ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS Deposited 1998-02-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–254（254 aa）
Chain B 1–254（254 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 1.92 Å R-free 0.238
1B14 Alcohol Dehydrogenase from Drosophila Lebanonensis Binary Complex with NAD+ Deposited 1998-11-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–254（254 aa）
Chain B 1–254（254 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；277 K；PROTEIN WAS CRYSTALLIZED FROM 28% PEG 2000, 0.2 M CACL2, 0.1 M TRIS-HCL, PH=7.0, 277 K.
Resolution 2.40 Å R-free 0.243
1B15 ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLEX WITH NAD-ACETONE Deposited 1998-11-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–254（254 aa）
Chain B 1–254（254 aa）
Not recorded NAE NICOTINAMIDE ADENINE DINUCLEOTIDE ACETONE ADDUCT × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 28% PEG 2000, 0.2 M CACL2, 0.1 M TRIS-HCL, PH=7.5, 1MM NAD+, 1% ACETONE, 277 K.
Resolution 2.20 Å R-free 0.258
1B2L ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS: TERNARY COMPLEX WITH NAD-CYCLOHEXANONE Deposited 1998-11-26 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 1–254（254 aa）
Not recorded CA CALCIUM ION × 2 NDC NICOTINAMIDE ADENINE DINUCLEOTIDE CYCLOHEXANONE × 2 CYH CYCLOHEXANONE × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；277 K；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 2000, 0.2 M CACL2, 0.1 M TRIS-HCL, PH= 8.0, 1MM NAD+, 1% CYCLOHEXANONE, 277 K.
Resolution 1.60 Å R-free 0.212
1SBY Alcohol dehydrogenase from Drosophila lebanonensis complexed with NAD+ and 2,2,2-trifluoroethanol at 1.1 A resolution Deposited 2004-02-11 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–254（254 aa）
Chain B 1–254（254 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 ETF TRIFLUOROETHANOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.2M CaCl2, 0.1M Tris/HCl, 28% w/v PEG 2000, 10mM NAD, 10mM 2,2,2-trifluoroethanol, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.10 Å R-free 0.172
3RJ5 Structure of alcohol dehydrogenase from Drosophila lebanonesis T114V mutant complexed with NAD+ Deposited 2011-04-15 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 1–254（254 aa）
Chain B 1–254（254 aa）
Mutation：T114V Mutation：T114V ACY ACETIC ACID × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；24.8% PEG (3350), 0.2M lithium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.45 Å R-free 0.239
3RJ9 Structure of alcohol dehydrogenase from Drosophila lebanonesis T114V mutant complexed with NAD+ Deposited 2011-04-15 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 1–254（254 aa）
Chain B 1–254（254 aa）
Mutation：T111V Mutation：T111V NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；24.8% PEG (3350), 0.2M lithium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.98 Å R-free 0.256
3RJ9 Structure of alcohol dehydrogenase from Drosophila lebanonesis T114V mutant complexed with NAD+ Deposited 2011-04-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–254（254 aa）
Chain D 1–254（254 aa）
Mutation：T111V Mutation：T111V NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；24.8% PEG (3350), 0.2M lithium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.98 Å R-free 0.256
3RJ9 Structure of alcohol dehydrogenase from Drosophila lebanonesis T114V mutant complexed with NAD+ Deposited 2011-04-15 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–254（254 aa）
Chain F 1–254（254 aa）
Mutation：T111V Mutation：T111V NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；24.8% PEG (3350), 0.2M lithium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.98 Å R-free 0.256

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADH_DROLE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–254； UniProt 1–254 Author chain B； PDBConstruct 1–254； UniProt 1–254

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 1b16

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1b16
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1b16
Deposition date deposition_date1998-11-25
Structure title titleALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLEX WITH NAD-3-PENTANONE
Keywords keywords;OXIDOREDUCTASE, DETOXIFICATION, METABOLISM, ALCOHOL DEHYDROGENASE, DROSOPHILA LEBANONENSIS, SHORT-CHAIN DEHYDROGENASES/REDUCTASES, TERNARY COMPLEX, NAD-3- PENTANONE ADDUCT ;; 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_guinier24.36 Å
Radius of gyration Rg (electron density) rg_electron23.47 Å
Forward intensity I(0) i050684300.00
Molecular weight molecular_weight57081.0 kDa
Excluded volume excluded_volume72212 ų
Envelope volume envelope_volume80860 ų
Hydration-shell volume shell_volume28485 ų
Envelope diameter envelope_diameter84.8 Å
Shell Rg shell_rg31.17 Å
Envelope Rg envelope_rg23.75 Å
Shape Rg shape_rg23.44 Å
Total Rg total_rg24.43 Å
Total atoms total_atoms4026
Residues n_residues508
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 dmax82.6 Å
Rg (real space) rg_real24.35 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real5.0680e+07
I(0) uncertainty (real space) i0_real_error6.0410e+05
Rg (reciprocal space) rg_reciprocal24.35 Å
I(0) (reciprocal space) i0_reciprocal50680000.0000
Solution quality estimate total_estimate0.8694
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5 Å
Skewness Skewness skewness0.406
Kurtosis Kurtosis kurtosis-0.184
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha22280000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.986
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1b16a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd1b16b_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (2 domains)

Domain ID domain_id1b16A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1b16B00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
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8. Citations (2)

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9. Files and Curves (10)