SAXSdb — 5ac1

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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	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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 1–501 Chain D； UniProt 1–501	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

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 5AC1	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 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 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
5AC0 ovis aries Aldehyde Dehydrogenase 1A1 in complex with a duocarmycin analog Deposited 2015-08-10	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	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 conditions	Resolution 1.90 Å R-free 0.197

3 other PDB entries and 4 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 Author chain C； PDBConstruct 1–501； UniProt 1–501 Author chain D； 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	5ac1
Deposition date deposition_date	2015-08-11
Structure title title	Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor
Keywords keywords	OXIDOREDUCTASE, OXIDATION-REDUCTION PROCESS, ALDEHYDE DEHYDROGENASE ACTIVITY; 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	43.05 Å
Radius of gyration Rg (electron density) rg_electron	42.89 Å
Forward intensity I(0) i0	696836000.00
Molecular weight molecular_weight	220440.0 kDa
Excluded volume excluded_volume	276660 Å³
Envelope volume envelope_volume	348240 Å³
Hydration-shell volume shell_volume	65846 Å³
Envelope diameter envelope_diameter	144.8 Å
Shell Rg shell_rg	49.69 Å
Envelope Rg envelope_rg	42.25 Å
Shape Rg shape_rg	42.89 Å
Total Rg total_rg	43.16 Å
Total atoms total_atoms	15493
Residues n_residues	1976
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	143.0 Å
Rg (real space) rg_real	43.05 Å
Rg uncertainty (real space) rg_real_error	1.42 Å
I(0) (real space) i0_real	6.9680e+08
I(0) uncertainty (real space) i0_real_error	1.3080e+07
Rg (reciprocal space) rg_reciprocal	43.05 Å
I(0) (reciprocal space) i0_reciprocal	696800000.0000
Solution quality estimate total_estimate	0.8908
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	46.4 Å
Skewness Skewness skewness	0.285
Kurtosis Kurtosis kurtosis	-0.526
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	183200000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.879

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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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	16433

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	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	4

Entity 3 Entity 3 non-polymer

Description description	;[[(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 ;
Molecular weight formula_weight	667.5 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	723

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5ac1a_
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	d5ac1b_
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	d5ac1c_
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	d5ac1d_
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 (8 domains)

Domain ID domain_id	5ac1A01
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	5ac1A02
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	5ac1B01
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	5ac1B02
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	5ac1C01
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	5ac1C02
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	5ac1D01
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	5ac1D02
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	188.336 Å
Unit-cell length b length_b	80.953 Å
Unit-cell length c length_c	172.331 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.080 Å
Low-resolution limit resolution_low	49.380 Å
R factor r_factor	0.2305
R_work r_work	0.2287
R_free r_free	0.2649

fit	/app/data/saxs_computation/ac/5ac1/5ac1.fit
pddf	/app/data/pr_computation/ac/5ac1/5ac1.pr.out
profile	/app/data/saxs_computation/ac/5ac1/5ac1.dat

Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor

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