SAXSdb — 5env

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alcohol dehydrogenase 1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 2–348 Chain B； UniProt 2–348	Not recorded	ZN ZINC ION × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 ETF TRIFLUOROETHANOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.4；298 K；100 MM SODIUM N-TRIS(HYDROXYMETHYL)METHYL-3-AMINOPROPANESULFONATE, 0.25 MM EDTA, 2 MM NAD+, 0.2 M 2,2,2-TRIFLUOROETHANOL, 1 MM YBCL3, 16 % POLYETHYETHYLENE GLYCOL 5000 MONOMETHYL ETHER, PH 8.4	Resolution 3.00 Å R-free 0.197

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 5ENV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4W6Z YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME Deposited 2014-08-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–348（347 aa） Chain B 2–348（347 aa）	Not recorded	ZN ZINC ION × 8 8ID NICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE × 2 ETF TRIFLUOROETHANOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；278 K；125 MM SODIUM N-TRIS(HYDROXYMETHYL) METHYL-3-AMINOPROPANE SULFONIC ACID, 1.7 MM NICOTINAMIDE 8- IODOADENINE DINUCLEOTIDE, 0.1 M 2,2,2-TRIFLUOROETHANOL, 0.16 MM EDTA, 10 MG/ML PROTEIN, 6% INITIAL POLYETHYLENE GLYCOL 5000 MONOMETHYL ETHER (FLUKA MPEG5000) IN DROP HANGING OVER 22-26% MPEG5000 AND 0.1 M 2,2,2-TRIFLUOROETHANOL. CRYSTALS WERE SOAKED IN SAME BUFFER WITH 30% W/V MPEG5000 WITH 0.5 M 2,2,2- TRIFLUOROETHANOL FOR FIVE DAYS BEFORE FREEZING AT 100 K., PH 8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K, PH 8.40	Resolution 2.40 Å R-free 0.222
4W6Z YEAST ALCOHOL DEHYDROGENASE I, SACCHAROMYCES CEREVISIAE FERMENTATIVE ENZYME Deposited 2014-08-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 2–348（347 aa） Chain D 2–348（347 aa）	Not recorded	ZN ZINC ION × 8 8ID NICOTINAMIDE-8-IODO-ADENINE-DINUCLEOTIDE × 2 ETF TRIFLUOROETHANOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；278 K；125 MM SODIUM N-TRIS(HYDROXYMETHYL) METHYL-3-AMINOPROPANE SULFONIC ACID, 1.7 MM NICOTINAMIDE 8- IODOADENINE DINUCLEOTIDE, 0.1 M 2,2,2-TRIFLUOROETHANOL, 0.16 MM EDTA, 10 MG/ML PROTEIN, 6% INITIAL POLYETHYLENE GLYCOL 5000 MONOMETHYL ETHER (FLUKA MPEG5000) IN DROP HANGING OVER 22-26% MPEG5000 AND 0.1 M 2,2,2-TRIFLUOROETHANOL. CRYSTALS WERE SOAKED IN SAME BUFFER WITH 30% W/V MPEG5000 WITH 0.5 M 2,2,2- TRIFLUOROETHANOL FOR FIVE DAYS BEFORE FREEZING AT 100 K., PH 8.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K, PH 8.40	Resolution 2.40 Å R-free 0.222
7NTM Cryo-EM structure of S.cerevisiae native alcohol dehydrogenase 1 (ADH1) in its tetrameric apo state Deposited 2021-03-10	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–348（347 aa） Chain B 2–348（347 aa） Chain C 2–348（347 aa） Chain D 2–348（347 aa）	Not recorded	ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ADH1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–347； UniProt 2–348 Author chain B； PDBConstruct 1–347； UniProt 2–348

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5env
Deposition date deposition_date	2015-11-09
Structure title title	YEAST ALCOHOL DEHYDROGENASE WITH BOUND COENZYME
Keywords keywords	TETRAMER, ROSSMANN, NAD, ALCOHOL, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	29.38 Å
Radius of gyration Rg (electron density) rg_electron	29.41 Å
Forward intensity I(0) i0	92107500.00
Molecular weight molecular_weight	75217.0 kDa
Excluded volume excluded_volume	93750 Å³
Envelope volume envelope_volume	114560 Å³
Hydration-shell volume shell_volume	33142 Å³
Envelope diameter envelope_diameter	107.3 Å
Shell Rg shell_rg	35.89 Å
Envelope Rg envelope_rg	29.72 Å
Shape Rg shape_rg	29.44 Å
Total Rg total_rg	29.89 Å
Total atoms total_atoms	5268
Residues n_residues	694
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	102.6 Å
Rg (real space) rg_real	29.52 Å
Rg uncertainty (real space) rg_real_error	0.93 Å
I(0) (real space) i0_real	9.2110e+07
I(0) uncertainty (real space) i0_real_error	1.3980e+06
Rg (reciprocal space) rg_reciprocal	29.46 Å
I(0) (reciprocal space) i0_reciprocal	92100000.0000
Solution quality estimate total_estimate	0.7657
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.500
Kurtosis Kurtosis kurtosis	-0.259
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	40850000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.690; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Alcohol dehydrogenase 1
Molecular weight formula_weight	36759.9 kDa
EC 编号 ec_number	1.1.1.1
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5292

SIPETQKGVIFYESHGKLEYKDIPVPKPKANELLINVKYSGVCHTDLHAWHGDWPLPVKLPLVGGHEGAGVVVGMGENVKGWKIGDYAGIKWLNGSCMACEYCELGNESNCPHADLSGYTHDGSFQQYATADAVQAAHIPQGTDLAQVAPILCAGITVYKALKSANLMAGHWVAISGAAGGLGSLAVQYAKAMGYRVLGIDGGEGKEELFRSIGGEVFIDFTKEKDIVGAVLKATDGGAHGVINVSVSEAAIEASTRYVRANGTTVLVGMPAGAKCCSDVFNQVVKSISIVGSYVGNRADTREALDFFARGLVKSPIKVVGLSTLPEIYEKMEKGQIVGRYVVDTSK

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	SACCHAROMYCES CEREVISIAE

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	TRIFLUOROETHANOL
Molecular weight formula_weight	100.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5envA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	5envA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	5envB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

Domain ID domain_id	5envB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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8. Citations (3)

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Unit-cell length a length_a	146.256 Å
Unit-cell length b length_b	146.256 Å
Unit-cell length c length_c	65.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.1346
R_work r_work	0.1317
R_free r_free	0.1965

fit	/app/data/saxs_computation/en/5env/5env.fit
pddf	/app/data/pr_computation/en/5env/5env.pr.out
profile	/app/data/saxs_computation/en/5env/5env.dat

YEAST ALCOHOL DEHYDROGENASE WITH BOUND COENZYME

1. Protein Identity and Related Structures Protein Identity & Related Structures

Alcohol dehydrogenase 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction