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1deh

CRYSTALLIZATION OF HUMAN BETA1 ALCOHOL DEHYDROGENASE (15 MG/ML) IN 50 MM SODIUM PHOSPHATE (PH 7.5), 2.0 MM NAD+ AND 1 MM 4-IODOPYRAZOLE AT 25 OC, 13% (W/V) PEG 8000

Method: X-RAY DIFFRACTION Dmax: 103.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HUMAN BETA1 ALCOHOL DEHYDROGENASE

Homo sapiens

UniProt P00325

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 1–374 Chain B； UniProt 1–374 Not recorded ZN ZINC ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 PYZ 4-IODOPYRAZOLE × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5 Resolution 2.20 Å R-free 0.261

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 1DEH Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1HDX THREE-DIMENSIONAL STRUCTURES OF THREE HUMAN ALCOHOL DEHYDROGENASE VARIANTS: CORRELATIONS WITH THEIR FUNCTIONAL DIFFERENCES Deposited 1993-10-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded ZN ZINC ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 CXL CYCLOHEXANOL × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1HDY THREE-DIMENSIONAL STRUCTURES OF THREE HUMAN ALCOHOL DEHYDROGENASE VARIANTS: CORRELATIONS WITH THEIR FUNCTIONAL DIFFERENCES Deposited 1993-10-15 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–375（374 aa）
Chain B 2–375（374 aa）
Not recorded ZN ZINC ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 PYZ 4-IODOPYRAZOLE × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1HDZ THREE-DIMENSIONAL STRUCTURES OF THREE HUMAN ALCOHOL DEHYDROGENASE VARIANTS: CORRELATIONS WITH THEIR FUNCTIONAL DIFFERENCES Deposited 1993-10-15 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded ZN ZINC ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.50 Å
1HSZ HUMAN BETA-1 ALCOHOL DEHYDROGENASE (ADH1B*1) Deposited 2000-12-27 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–374（374 aa） Fragment：BETA SUBUNIT
Chain B 1–374（374 aa） Fragment：BETA SUBUNIT
Not recorded ZN ZINC ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；50 mM sodium phosphate, 2 mM NAD+, 14% (w/v) PEG 8000, 14 mg/ml protein, pH 7.5, VAPOR DIFFUSION, SITTING DROP at 277K
Resolution 2.20 Å R-free 0.257
1HTB CRYSTALLIZATION OF HUMAN BETA3 ALCOHOL DEHYDROGENASE (10 MG/ML) IN 100 MM SODIUM PHOSPHATE (PH 7.5), 7.5 MM NAD+ AND 1 MM 4-IODOPYRAZOLE AT 25 C Deposited 1995-08-10 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–375（374 aa）
Chain B 2–375（374 aa）
Not recorded ZN ZINC ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 PYZ 4-IODOPYRAZOLE × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.40 Å R-free 0.243
1U3U Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Benzylformamide Determined to 1.6 Angstrom Resolution Deposited 2004-07-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded ZN ZINC ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 BNF N-BENZYLFORMAMIDE × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；15mg/ml enzyme, 2mM NAD+, 50mM sodium phosphate, and 11.5-13% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.60 Å R-free 0.190
1U3V Crystal Structure of Human Alcohol Dehydrogenase Beta-1-Beta-1 Isoform Complexed with N-Heptylformamide Determined to 1.65 Angstrom Resolution Deposited 2004-07-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded ZN ZINC ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 HPL HEPTYLFORMAMIDE × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；15mg/ml enzyme, 2mM NAD+, 50mM sodium phosphate, and 11.5-13% PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 1.65 Å R-free 0.185
3HUD THE STRUCTURE OF HUMAN BETA 1 BETA 1 ALCOHOL DEHYDROGENASE: CATALYTIC EFFECTS OF NON-ACTIVE-SITE SUBSTITUTIONS Deposited 1993-01-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–374（374 aa）
Chain B 1–374（374 aa）
Not recorded ZN ZINC ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADHB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–374； UniProt 1–374 Author chain B； PDBConstruct 1–374； UniProt 1–374

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 1deh

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1deh
Deposition date deposition_date1995-10-14
Structure title titleCRYSTALLIZATION OF HUMAN BETA1 ALCOHOL DEHYDROGENASE (15 MG/ML) IN 50 MM SODIUM PHOSPHATE (PH 7.5), 2.0 MM NAD+ AND 1 MM 4-IODOPYRAZOLE AT 25 OC, 13% (W/V) PEG 8000
Keywords keywordsNAD+ DEPENDENT ALCOHOL DEHYDROGENASE, 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_guinier29.65 Å
Radius of gyration Rg (electron density) rg_electron29.70 Å
Forward intensity I(0) i0105222000.00
Molecular weight molecular_weight81473.0 kDa
Excluded volume excluded_volume102040 ų
Envelope volume envelope_volume119480 ų
Hydration-shell volume shell_volume34355 ų
Envelope diameter envelope_diameter109.5 Å
Shell Rg shell_rg36.10 Å
Envelope Rg envelope_rg29.90 Å
Shape Rg shape_rg29.73 Å
Total Rg total_rg30.13 Å
Total atoms total_atoms5667
Residues n_residues748
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 dmax103.4 Å
Rg (real space) rg_real29.80 Å
Rg uncertainty (real space) rg_real_error1.02 Å
I(0) (real space) i0_real1.0520e+08
I(0) uncertainty (real space) i0_real_error1.6870e+06
Rg (reciprocal space) rg_reciprocal29.74 Å
I(0) (reciprocal space) i0_reciprocal105200000.0000
Solution quality estimate total_estimate0.8493
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.3 Å
Skewness Skewness skewness0.502
Kurtosis Kurtosis kurtosis-0.273
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha52610000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.731; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.985
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1deha1
Class classb — All beta proteins
Fold Fold foldb.35 — GroES-like
Superfamily Superfamily superfamilyb.35.1 — GroES-like
Family Family familyb.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain
Domain ID domain_idd1deha2
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain
Domain ID domain_idd1dehb1
Class classb — All beta proteins
Fold Fold foldb.35 — GroES-like
Superfamily Superfamily superfamilyb.35.1 — GroES-like
Family Family familyb.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain
Domain ID domain_idd1dehb2
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id1dehA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Medium-chain alcohol dehydrogenases, catalytic domain
Domain ID domain_id1dehA02
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_id1dehB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Medium-chain alcohol dehydrogenases, catalytic domain
Domain ID domain_id1dehB02
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)