SAXSdb — 1y9a

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

NADP-dependent alcohol dehydrogenase

Entamoeba histolytica

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 1–360 Chain C； UniProt 1–360	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 CAC CACODYLATE ION × 4 ACT ACETATE ION × 4 MG MAGNESIUM ION × 4 EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 8000 14%w/v, 300 mM Mg Acetate, 200mM cacodylate at pH 6.5, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.81 Å R-free 0.177

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 1Y9A	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OUI D275P mutant of alcohol dehydrogenase from protozoa Entamoeba histolytica Deposited 2007-02-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–360（360 aa） Chain B 1–360（360 aa） Chain C 1–360（360 aa） Chain D 1–360（360 aa）	Mutation：D275P Mutation：D275P Mutation：D275P Mutation：D275P	ZN ZINC ION × 4 NO3 NITRATE ION × 4 CAC CACODYLATE ION × 4 EDO 1,2-ETHANEDIOL × 9 PGE TRIETHYLENE GLYCOL × 4 1PE PENTAETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；8mg/mL protein, 25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.77 Å R-free 0.178
3FPC Chimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica ADH Deposited 2009-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 153–294（142 aa） Chain B 153–294（142 aa） Chain C 153–294（142 aa） Chain D 153–294（142 aa）	Not recorded	ZN ZINC ION × 4 CAC CACODYLATE ION × 4 OXY OXYGEN MOLECULE × 1 EDO 1,2-ETHANEDIOL × 14 NO3 NITRATE ION × 2 IMD IMIDAZOLE × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；8mg/mL protein [25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2 (pH=7.5)] was mixed with 0.001 ml of reservoir solution [16% (w/v) PEG 8000, 200mM magnesium acetate tetrahydrate, 100mM Cacodylate buffer (pH 6.5)], vapor diffusion, hanging drop, temperature 298K	Resolution 1.40 Å R-free 0.155

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

View Construct and Data Evidence

UniProt name	ADH1_ENTHI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–360； UniProt 1–360 Author chain C； PDBConstruct 1–360； UniProt 1–360

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	1y9a
Deposition date deposition_date	2004-12-15
Structure title title	Alcohol Dehydrogenase from Entamoeba histolotica in complex with cacodylate
Keywords keywords	Metal-binding, NADP, 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	29.73 Å
Radius of gyration Rg (electron density) rg_electron	28.91 Å
Forward intensity I(0) i0	100587000.00
Molecular weight molecular_weight	78290.0 kDa
Excluded volume excluded_volume	97811 Å³
Envelope volume envelope_volume	121540 Å³
Hydration-shell volume shell_volume	34659 Å³
Envelope diameter envelope_diameter	90.1 Å
Shell Rg shell_rg	36.70 Å
Envelope Rg envelope_rg	28.59 Å
Shape Rg shape_rg	28.90 Å
Total Rg total_rg	29.68 Å
Total atoms total_atoms	5462
Residues n_residues	718
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	92.2 Å
Rg (real space) rg_real	29.66 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	1.0060e+08
I(0) uncertainty (real space) i0_real_error	1.4580e+06
Rg (reciprocal space) rg_reciprocal	29.69 Å
I(0) (reciprocal space) i0_reciprocal	100600000.0000
Solution quality estimate total_estimate	0.7121
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.3 Å
Skewness Skewness skewness	0.179
Kurtosis Kurtosis kurtosis	-0.697
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	32530000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.998; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	NADP-dependent alcohol dehydrogenase
Molecular weight formula_weight	38697.6 kDa
EC 编号 ec_number	1.1.1.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	6218

MKGLAMLGIGRIGWIEKKIPECGPLDALVRPLALAPCTSDTHTVWAGAIGDRHDMILGHEAVGQIVKVGSLVKRLKVGDKVIVPAITPDWGEEESQRGYPMHSGGMLGGWKFSNFKDGVFSEVFHVNEADANLALLPRDIKPEDAVMLSDMVTTGFHGAELANIKLGDTVCVIGIGPVGLMSVAGANHLGAGRIFAVGSRKHCCDIALEYGATDIINYKNGDIVEQILKATDGKGVDKVVIAGGDVHTFAQAVKMIKPGSDIGNVNYLGEGDNIDIPRSEWGVGMGHKHIHGGLTPGGRVRMEKLASLISTGKLDTSKLITHRFEGLEKVEDALMLMKNKPADLIKPVVRIHYDDEDTLH

来源 Source

来源生物 organism	Entamoeba histolytica
NCBI Class编号 ncbi_taxonomy_id	5759
宿主生物 host_organism	Escherichia coli

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	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	754

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	1y9aA01
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	1y9aA02
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	1y9aC01
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	1y9aC02
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 (2)

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Unit-cell length a length_a	76.891 Å
Unit-cell length b length_b	234.139 Å
Unit-cell length c length_c	96.241 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	117.040 Å
R factor r_factor	0.1288
R_work r_work	0.1263
R_free r_free	0.1771

fit	/app/data/saxs_computation/y9/1y9a/1y9a.fit
pddf	/app/data/pr_computation/y9/1y9a/1y9a.pr.out
profile	/app/data/saxs_computation/y9/1y9a/1y9a.dat

Alcohol Dehydrogenase from Entamoeba histolotica in complex with cacodylate