SAXSdb — 5ac0

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

RETINAL DEHYDROGENASE 1

OVIS ARIES

UniProt P51977

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 1–501 Chain B； UniProt 1–501	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 K9P 1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 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 5AC0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BXS SHEEP LIVER CLASS 1 ALDEHYDE DEHYDROGENASE WITH NAD BOUND Deposited 1998-10-08	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 1–500（500 aa） Chain B 1–500（500 aa） Chain C 1–500（500 aa） Chain D 1–500（500 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2	Resolution 2.35 Å R-free 0.259
5ABM Sheep aldehyde dehydrogenase 1A1 Deposited 2015-08-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 2–501（500 aa） Fragment：UNP RESIDUES 2-501 Chain D 2–501（500 aa） Fragment：UNP RESIDUES 2-501	Not recorded	TXE [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；100 MM BIS-TRIS, PH 6.0, 4.5-7% PEG5000, 150=225MM MGCL2, 4DEGREE	Resolution 1.70 Å R-free 0.203
5ABM Sheep aldehyde dehydrogenase 1A1 Deposited 2015-08-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–501（500 aa） Fragment：UNP RESIDUES 2-501 Chain B 2–501（500 aa） Fragment：UNP RESIDUES 2-501	Not recorded	TXE [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；100 MM BIS-TRIS, PH 6.0, 4.5-7% PEG5000, 150=225MM MGCL2, 4DEGREE	Resolution 1.70 Å R-free 0.203
5AC1 Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor Deposited 2015-08-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–501（501 aa） Chain B 1–501（501 aa）	Not recorded	K9P 1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one × 4 TXE [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；100 MM BIS-TRIS, PH 6.0, 4.5-7% PEG5000, 150=225MM MGCL2, 4DEGREE	Resolution 2.08 Å R-free 0.265
5AC1 Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor Deposited 2015-08-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain C 1–501（501 aa） Chain D 1–501（501 aa）	Not recorded	K9P 1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one × 4 TXE [[(2R,3S,4R,5R)-5-[(3R)-3-aminocarbonyl-3,4-dihydro-2H-pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-ph osphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；100 MM BIS-TRIS, PH 6.0, 4.5-7% PEG5000, 150=225MM MGCL2, 4DEGREE	Resolution 2.08 Å R-free 0.265

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AL1A1_SHEEP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–501； UniProt 1–501 Author chain B； PDBConstruct 1–501； UniProt 1–501

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	5ac0
Deposition date deposition_date	2015-08-10
Structure title title	ovis aries Aldehyde Dehydrogenase 1A1 in complex with a duocarmycin analog
Keywords keywords	OXIDOREDUCTASE, ALDEHYDE DEHYDROGENASE ACTIVITY, OXIDATION-REDUCTION PROCESS; 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	30.48 Å
Radius of gyration Rg (electron density) rg_electron	29.95 Å
Forward intensity I(0) i0	186443000.00
Molecular weight molecular_weight	110060.0 kDa
Excluded volume excluded_volume	138130 Å³
Envelope volume envelope_volume	159570 Å³
Hydration-shell volume shell_volume	43339 Å³
Envelope diameter envelope_diameter	98.1 Å
Shell Rg shell_rg	38.19 Å
Envelope Rg envelope_rg	30.08 Å
Shape Rg shape_rg	29.95 Å
Total Rg total_rg	30.62 Å
Total atoms total_atoms	7736
Residues n_residues	988
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	98.3 Å
Rg (real space) rg_real	30.42 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.8640e+08
I(0) uncertainty (real space) i0_real_error	2.7510e+06
Rg (reciprocal space) rg_reciprocal	30.45 Å
I(0) (reciprocal space) i0_reciprocal	186400000.0000
Solution quality estimate total_estimate	0.8924
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.0 Å
Skewness Skewness skewness	0.316
Kurtosis Kurtosis kurtosis	-0.412
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	61940000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.929

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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	RETINAL DEHYDROGENASE 1
Molecular weight formula_weight	54885.6 kDa
EC 编号 ec_number	1.2.1.36
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	8593

MSSSAMPDVPAPLTNLQFKYTKIFINNEWHSSVSGKKFPVFNPATEEKLCEVEEGDKEDVDKAVKAARQAFQIGSPWRTMDASERGRLLNKLADLIERDRLLLATMEAMNGGKLFSNAYLMDLGGCIKTLRYCAGWADKIQGRTIPMDGNFFTYTRSEPVGVCGQIIPWNFPLLMFLWKIGPALSCGNTVVVKPAEQTPLTALHMGSLIKEAGFPPGVVNIVPGYGPTAGAAISSHMDVDKVAFTGSTEVGKLIKEAAGKSNLKRVSLELGGKSPCIVFADADLDNAVEFAHQGVFYHQGQCCIAASRLFVEESIYDEFVRRSVERAKKYVLGNPLTPGVSQGPQIDKEQYEKILDLIESGKKEGAKLECGGGPWGNKGYFIQPTVFSDVTDDMRIAKEEIFGPVQQIMKFKSLDDVIKRANNTFYGLSAGIFTNDIDKAITVSSALQSGTVWVNCYSVVSAQCPFGGFKMSGNGRELGEYGFHEYTEVKTVTIKISQKNS

来源 Source

来源生物 organism	OVIS ARIES
通用名 common_name	SHEEP
NCBI Class编号 ncbi_taxonomy_id	9940
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 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 3 Entity 3 non-polymer

Description description	1-[(1S)-1-methyl-5-oxidanyl-1,2-dihydrobenzo[e]indol-3-yl]hexan-1-one
Molecular weight formula_weight	297.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	698

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5ac0a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.82 — ALDH-like
Superfamily Superfamily superfamily	c.82.1 — ALDH-like
Family Family family	c.82.1.1 — ALDH-like

Domain ID domain_id	d5ac0b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.82 — ALDH-like
Superfamily Superfamily superfamily	c.82.1 — ALDH-like
Family Family family	c.82.1.1 — ALDH-like

CATH v4.4 (4 domains)

Domain ID domain_id	5ac0A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

Domain ID domain_id	5ac0A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

Domain ID domain_id	5ac0B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 1

Domain ID domain_id	5ac0B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Aldehyde Dehydrogenase; Chain A, domain 2

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8. Citations (1)

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Unit-cell length a length_a	93.556 Å
Unit-cell length b length_b	150.644 Å
Unit-cell length c length_c	80.677 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	50.210 Å
R factor r_factor	0.1556
R_work r_work	0.1534
R_free r_free	0.1967

fit	/app/data/saxs_computation/ac/5ac0/5ac0.fit
pddf	/app/data/pr_computation/ac/5ac0/5ac0.pr.out
profile	/app/data/saxs_computation/ac/5ac0/5ac0.dat

ovis aries Aldehyde Dehydrogenase 1A1 in complex with a duocarmycin analog

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

RETINAL 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