SAXSdb — 1cdo

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

ALCOHOL DEHYDROGENASE

OrganismNot specified

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	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.05 Å R-free 0.248

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	ADH_GADCA
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cdo
Deposition date deposition_date	1995-09-29
Structure title title	ALCOHOL DEHYDROGENASE (E.C.1.1.1.1) (EE ISOZYME) COMPLEXED WITH NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD), AND ZINC
Keywords keywords	OXIDOREDUCTASE, OXIDOREDUCTASE (CH-OH(D)-NAD(A)); OXIDOREDUCTASE (CH-OH(D)-NAD(A))
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	30.20 Å
Radius of gyration Rg (electron density) rg_electron	30.26 Å
Forward intensity I(0) i0	106115000.00
Molecular weight molecular_weight	81591.0 kDa
Excluded volume excluded_volume	102120 Å³
Envelope volume envelope_volume	123150 Å³
Hydration-shell volume shell_volume	34935 Å³
Envelope diameter envelope_diameter	111.4 Å
Shell Rg shell_rg	36.40 Å
Envelope Rg envelope_rg	30.23 Å
Shape Rg shape_rg	30.27 Å
Total Rg total_rg	30.78 Å
Total atoms total_atoms	5698
Residues n_residues	748
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	104.8 Å
Rg (real space) rg_real	30.36 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	1.0610e+08
I(0) uncertainty (real space) i0_real_error	1.8210e+06
Rg (reciprocal space) rg_reciprocal	30.29 Å
I(0) (reciprocal space) i0_reciprocal	106100000.0000
Solution quality estimate total_estimate	0.8502
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.2 Å
Skewness Skewness skewness	0.500
Kurtosis Kurtosis kurtosis	-0.279
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	47870000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.748; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.853; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ALCOHOL DEHYDROGENASE
Molecular weight formula_weight	40049.4 kDa
EC 编号 ec_number	1.1.1.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6346

ATVGKVIKCKAAVAWEANKPLVIEEIEVDVPHANEIRIKIIATGVCHTDLYHLFEGKHKDGFPVVLGHEGAGIVESVGPGVTEFQPGEKVIPLFISQCGECRFCQSPKTNQCVKGWANESPDVMSPKETRFTCKGRKVLQFLGTSTFSQYTVVNQIAVAKIDPSAPLDTVCLLGCGVSTGFGAAVNTAKVEPGSTCAVFGLGAVGLAAVMGCHSAGAKRIIAVDLNPDKFEKAKVFGATDFVNPNDHSEPISQVLSKMTNGGVDFSLECVGNVGVMRNALESCLKGWGVSVLVGWTDLHDVATRPIQLIAGRTWKGSMFGGFKGKDGVPKMVKAYLDKKVKLDEFITHRMPLESVNDAIDLMKHGKCIRTVLSL

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	648

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1cdoa1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cdoa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

Domain ID domain_id	d1cdob1
Class class	b — All beta proteins
Fold Fold fold	b.35 — GroES-like
Superfamily Superfamily superfamily	b.35.1 — GroES-like
Family Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

Domain ID domain_id	d1cdob2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

CATH v4.4 (4 domains)

Domain ID domain_id	1cdoA01
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	1cdoA02
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	1cdoB01
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	1cdoB02
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	102.950 Å
Unit-cell length b length_b	47.600 Å
Unit-cell length c length_c	80.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.1770
R_work r_work	0.1770
R_free r_free	0.2480

fit	/app/data/saxs_computation/cd/1cdo/1cdo.fit
pddf	/app/data/pr_computation/cd/1cdo/1cdo.pr.out
profile	/app/data/saxs_computation/cd/1cdo/1cdo.dat

ALCOHOL DEHYDROGENASE (E.C.1.1.1.1) (EE ISOZYME) COMPLEXED WITH NICOTINAMIDE ADENINE DINUCLEOTIDE (NAD), AND ZINC

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

ALCOHOL DEHYDROGENASE

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