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3rj5

Structure of alcohol dehydrogenase from Drosophila lebanonesis T114V mutant complexed with NAD+

Method: X-RAY DIFFRACTION Dmax: 86.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alcohol dehydrogenase

Scaptodrosophila lebanonensis

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 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

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 3RJ5 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 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）
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 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）
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 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）
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
1B16 ALCOHOL DEHYDROGENASE FROM DROSOPHILA LEBANONENSIS TERNARY COMPLEX WITH NAD-3-PENTANONE Deposited 1998-11-25 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）
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
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 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）
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
3RJ9 Structure of alcohol dehydrogenase from Drosophila lebanonesis T114V mutant complexed with NAD+ Deposited 2011-04-15 Different mutation/modification Different ligand/ion 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 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 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 3rj5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3rj5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3rj5
Deposition date deposition_date2011-04-15
Structure title titleStructure of alcohol dehydrogenase from Drosophila lebanonesis T114V mutant complexed with NAD+
Keywords keywordsshort-chain dehydrogenases/reductases, oxidoreductase, detoxification, NAD metabolism; 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_guinier24.49 Å
Radius of gyration Rg (electron density) rg_electron23.61 Å
Forward intensity I(0) i048079300.00
Molecular weight molecular_weight55828.0 kDa
Excluded volume excluded_volume70782 ų
Envelope volume envelope_volume80693 ų
Hydration-shell volume shell_volume28379 ų
Envelope diameter envelope_diameter89.2 Å
Shell Rg shell_rg31.01 Å
Envelope Rg envelope_rg23.82 Å
Shape Rg shape_rg23.57 Å
Total Rg total_rg24.56 Å
Total atoms total_atoms3940
Residues n_residues504
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 dmax86.1 Å
Rg (real space) rg_real24.49 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real4.8080e+07
I(0) uncertainty (real space) i0_real_error6.6460e+05
Rg (reciprocal space) rg_reciprocal24.49 Å
I(0) (reciprocal space) i0_reciprocal48080000.0000
Solution quality estimate total_estimate0.8523
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3 Å
Skewness Skewness skewness0.404
Kurtosis Kurtosis kurtosis-0.188
Angular range angular_range— – 0.3250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha18490000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.711; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.999
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3rj5a_
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_idd3rj5b_
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_id3rj5A00
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_id3rj5B00
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 (1)

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9. Files and Curves (10)