SAXSdb — 5ky6

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

Fructose-bisphosphate aldolase A

Homo sapiens

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 2–364 Chain B； UniProt 2–364 Chain C； UniProt 2–364 Chain D； UniProt 2–364	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；292 K；1.6M ammonium citrate tribasic	Resolution 1.94 Å R-free 0.223

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 5KY6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ALD ACTIVITY AND SPECIFICITY OF HUMAN ALDOLASES Deposited 1991-05-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
2ALD HUMAN MUSCLE ALDOLASE Deposited 1998-10-21	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–363（363 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.10 Å R-free 0.258
4ALD HUMAN MUSCLE FRUCTOSE 1,6-BISPHOSPHATE ALDOLASE COMPLEXED WITH FRUCTOSE 1,6-BISPHOSPHATE Deposited 1998-07-26	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 1–363（363 aa）	Not recorded	2FP 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.80 Å R-free 0.304
6XMH Human aldolase A wild type Deposited 2020-06-30	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 1–364（364 aa） Chain B 1–364（364 aa）	Not recorded	PO4 PHOSPHATE ION × 8 GOL GLYCEROL × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.75；277 K；10% (w/v) PEG 8,000, 18% (v/v) glycerol, 0.04 M potassium phosphate, pH 5.75	Resolution 1.95 Å R-free 0.286
6XML Human aldolase A I98C Deposited 2020-06-30	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 1–364（364 aa） Chain B 1–364（364 aa）	Mutation：I98C Mutation：I98C	PO4 PHOSPHATE ION × 8 GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；10% (w/v) PEG 8000, 21% (v/v) glycerol in 0.04 M potassium phosphate, pH 6.0	Resolution 1.88 Å R-free 0.286
6XMM Human aldolase A I98S Deposited 2020-06-30	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 1–364（364 aa） Chain B 1–364（364 aa）	Mutation：I98S Mutation：I98S	PO4 PHOSPHATE ION × 8 GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；10% (w/v) PEG 8000, 15% (v/v) glycerol, 0.04 M potassium phosphate, pH 6.0	Resolution 2.11 Å R-free 0.295
6XMO Human aldolase A I98F Deposited 2020-06-30	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 1–364（364 aa） Chain B 1–364（364 aa）	Mutation：I98F Mutation：I98F	PO4 PHOSPHATE ION × 8 GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.75；277 K；12% (w/v) PEG 8000, 15% (v/v) glycerol, 0.04 M potassium phosphate, pH 5.75	Resolution 2.60 Å R-free 0.259

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ALDOA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–363； UniProt 2–364 Author chain B； PDBConstruct 1–363； UniProt 2–364 Author chain C； PDBConstruct 1–363； UniProt 2–364 Author chain D； PDBConstruct 1–363； UniProt 2–364

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	5ky6
Deposition date deposition_date	2016-07-21
Structure title title	Human muscle fructose-1,6-bisphosphate aldolase
Keywords keywords	aldolase, muscle, glycolysis, glyconeogenesis, lyase; LYASE
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	34.30 Å
Radius of gyration Rg (electron density) rg_electron	33.39 Å
Forward intensity I(0) i0	313739000.00
Molecular weight molecular_weight	143330.0 kDa
Excluded volume excluded_volume	179740 Å³
Envelope volume envelope_volume	218020 Å³
Hydration-shell volume shell_volume	53329 Å³
Envelope diameter envelope_diameter	117.9 Å
Shell Rg shell_rg	41.25 Å
Envelope Rg envelope_rg	33.44 Å
Shape Rg shape_rg	33.39 Å
Total Rg total_rg	33.91 Å
Total atoms total_atoms	20236
Residues n_residues	1318
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	107.2 Å
Rg (real space) rg_real	34.17 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	3.1370e+08
I(0) uncertainty (real space) i0_real_error	4.6790e+06
Rg (reciprocal space) rg_reciprocal	34.25 Å
I(0) (reciprocal space) i0_reciprocal	313800000.0000
Solution quality estimate total_estimate	0.8955
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.9 Å
Skewness Skewness skewness	0.204
Kurtosis Kurtosis kurtosis	-0.441
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	56520000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.849

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5ky6a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d5ky6b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d5ky6c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d5ky6d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

CATH v4.4 (4 domains)

Domain ID domain_id	5ky6A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5ky6B00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5ky6C00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

Domain ID domain_id	5ky6D00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

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8. Citations (2)

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Unit-cell length a length_a	84.511 Å
Unit-cell length b length_b	57.253 Å
Unit-cell length c length_c	164.016 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.57 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.941 Å
Low-resolution limit resolution_low	46.721 Å
R factor r_factor	0.1867
R_work r_work	0.1864
R_free r_free	0.2227

Description description	Fructose-bisphosphate aldolase A
Molecular weight formula_weight	39338.8 kDa
EC 编号 ec_number	4.1.2.13
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	20854

Human muscle fructose-1,6-bisphosphate aldolase

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

Fructose-bisphosphate aldolase A

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	562

fit	/app/data/saxs_computation/ky/5ky6/5ky6.fit
pddf	/app/data/pr_computation/ky/5ky6/5ky6.pr.out
profile	/app/data/saxs_computation/ky/5ky6/5ky6.dat