SAXSdb — 5abm

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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 C； UniProt 2–501 Chain D； UniProt 2–501	Fragment：UNP RESIDUES 2-501	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
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–501 Chain B； UniProt 2–501	Fragment：UNP RESIDUES 2-501	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

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 5ABM	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
5AC0 ovis aries Aldehyde Dehydrogenase 1A1 in complex with a duocarmycin analog Deposited 2015-08-10	Different construct 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
5AC1 Sheep aldehyde dehydrogenase 1A1 with duocarmycin analog inhibitor Deposited 2015-08-11	Different construct Different ligand/ion 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 construct Different ligand/ion 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 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 1–500； UniProt 2–501 Author chain B； PDBConstruct 1–500； UniProt 2–501 Author chain C； PDBConstruct 1–500； UniProt 2–501 Author chain D； PDBConstruct 1–500； UniProt 2–501

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	5abm
Deposition date deposition_date	2015-08-07
Structure title title	Sheep aldehyde dehydrogenase 1A1
Keywords keywords	OXIDOREDUCTASE, OXIDATION-REDUCTION PROCESS, 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	42.94 Å
Radius of gyration Rg (electron density) rg_electron	42.78 Å
Forward intensity I(0) i0	695491000.00
Molecular weight molecular_weight	219250.0 kDa
Excluded volume excluded_volume	274850 Å³
Envelope volume envelope_volume	347000 Å³
Hydration-shell volume shell_volume	65934 Å³
Envelope diameter envelope_diameter	144.1 Å
Shell Rg shell_rg	49.44 Å
Envelope Rg envelope_rg	42.11 Å
Shape Rg shape_rg	42.78 Å
Total Rg total_rg	43.05 Å
Total atoms total_atoms	15405
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	140.6 Å
Rg (real space) rg_real	42.94 Å
Rg uncertainty (real space) rg_real_error	1.35 Å
I(0) (real space) i0_real	6.9550e+08
I(0) uncertainty (real space) i0_real_error	1.3380e+07
Rg (reciprocal space) rg_reciprocal	42.94 Å
I(0) (reciprocal space) i0_reciprocal	695500000.0000
Solution quality estimate total_estimate	0.8909
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	45.6 Å
Skewness Skewness skewness	0.287
Kurtosis Kurtosis kurtosis	-0.522
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	175500000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.827

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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	RETINAL DEHYDROGENASE 1
Molecular weight formula_weight	54754.4 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	16987

SSSAMPDVPAPLTNLQFKYTKIFINNEWHSSVSGKKFPVFNPATEEKLCEVEEGDKEDVDKAVKAARQAFQIGSPWRTMDASERGRLLNKLADLIERDRLLLATMEAMNGGKLFSNAYLMDLGGCIKTLRYCAGWADKIQGRTIPMDGNFFTYTRSEPVGVCGQIIPWNFPLLMFLWKIGPALSCGNTVVVKPAEQTPLTALHMGSLIKEAGFPPGVVNIVPGYGPTAGAAISSHMDVDKVAFTGSTEVGKLIKEAAGKSNLKRVSLELGGKSPCIVFADADLDNAVEFAHQGVFYHQGQCCIAASRLFVEESIYDEFVRRSVERAKKYVLGNPLTPGVSQGPQIDKEQYEKILDLIESGKKEGAKLECGGGPWGNKGYFIQPTVFSDVTDDMRIAKEEIFGPVQQIMKFKSLDDVIKRANNTFYGLSAGIFTNDIDKAITVSSALQSGTVWVNCYSVVSAQCPFGGFKMSGNGRELGEYGFHEYTEVKTVTIKISQKNS

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	;[[(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 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1340

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5abma_
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	d5abmb_
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	d5abmc_
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	d5abmd_
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	5abmA01
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	5abmA02
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	5abmB01
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	5abmB02
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	5abmC01
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	5abmC02
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	5abmD01
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	5abmD02
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	187.985 Å
Unit-cell length b length_b	80.804 Å
Unit-cell length c length_c	171.408 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.97 °
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	1.700 Å
Low-resolution limit resolution_low	151.850 Å
R factor r_factor	0.1813
R_work r_work	0.1801
R_free r_free	0.2027

fit	/app/data/saxs_computation/ab/5abm/5abm.fit
pddf	/app/data/pr_computation/ab/5abm/5abm.pr.out
profile	/app/data/saxs_computation/ab/5abm/5abm.dat

Sheep aldehyde dehydrogenase 1A1

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