SAXSdb — 5ax8

▼

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

Aspartate aminotransferase, mitochondrial

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 30–430 Chain C； UniProt 30–430	Fragment：UNP residues 40-430	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；0.1 M HEPES pH 6.8, 25% (v/v) Jeffamine ED-2001 pH 6.8	Resolution 2.99 Å R-free 0.291
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 30–430 Chain D； UniProt 30–430	Fragment：UNP residues 40-430	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；0.1 M HEPES pH 6.8, 25% (v/v) Jeffamine ED-2001 pH 6.8	Resolution 2.99 Å R-free 0.291

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 5AX8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8SKR human liver mitochondrial Aspartate aminotransferase Deposited 2023-04-20	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–430（430 aa） Chain C 1–430（430 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å
9YB6 Human Mitochondrial Aspartate Aminotransferase complex with PLP at 1.5 Angstrom. Deposited 2025-09-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–430（430 aa） Chain B 1–430（430 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 5 SO4 SULFATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M Ammonium Sulfate, 0.05 M Sodium Acetate, 23% PEG-3350, pH 5.5	Resolution 1.50 Å R-free 0.209

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AATM_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–401； UniProt 30–430 Author chain B； PDBConstruct 1–401； UniProt 30–430 Author chain C； PDBConstruct 1–401； UniProt 30–430 Author chain D； PDBConstruct 1–401； UniProt 30–430

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ax8
Deposition date deposition_date	2015-07-20
Structure title title	Recombinant expression, purification and preliminary crystallographic studies of the mature form of human mitochondrial aspartate aminotransferase
Keywords keywords	;aspartate aminotransferase, plasma membrane fatty acid binding protein, kynurenine aminotransferase-IV, three-dimensional structure, TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	38.99 Å
Radius of gyration Rg (electron density) rg_electron	38.58 Å
Forward intensity I(0) i0	473968000.00
Molecular weight molecular_weight	178750.0 kDa
Excluded volume excluded_volume	224200 Å³
Envelope volume envelope_volume	278590 Å³
Hydration-shell volume shell_volume	60133 Å³
Envelope diameter envelope_diameter	145.4 Å
Shell Rg shell_rg	44.47 Å
Envelope Rg envelope_rg	38.26 Å
Shape Rg shape_rg	38.58 Å
Total Rg total_rg	38.91 Å
Total atoms total_atoms	12580
Residues n_residues	1604
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	135.5 Å
Rg (real space) rg_real	39.06 Å
Rg uncertainty (real space) rg_real_error	1.34 Å
I(0) (real space) i0_real	4.7400e+08
I(0) uncertainty (real space) i0_real_error	9.7670e+06
Rg (reciprocal space) rg_reciprocal	39.02 Å
I(0) (reciprocal space) i0_reciprocal	473900000.0000
Solution quality estimate total_estimate	0.8666
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	46.3 Å
Skewness Skewness skewness	0.430
Kurtosis Kurtosis kurtosis	-0.160
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	96660000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.789; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.905

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5ax8a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.1 — AAT-like

Domain ID domain_id	d5ax8b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.1 — AAT-like

Domain ID domain_id	d5ax8c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.1 — AAT-like

Domain ID domain_id	d5ax8d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.1 — AAT-like

CATH v4.4 (8 domains)

Domain ID domain_id	5ax8A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	5ax8A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	5ax8B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	5ax8B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	5ax8C01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	5ax8C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	5ax8D01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

Domain ID domain_id	5ax8D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

▶

8. Citations (1)

▶

Unit-cell length a length_a	56.706 Å
Unit-cell length b length_b	76.140 Å
Unit-cell length c length_c	94.247 Å
Unit-cell angle α angle_alpha	78.00 °
Unit-cell angle β angle_beta	85.65 °
Unit-cell angle γ angle_gamma	78.41 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.989 Å
Low-resolution limit resolution_low	48.315 Å
R factor r_factor	0.2740
R_work r_work	0.2726
R_free r_free	0.2913

Description description	Aspartate aminotransferase, mitochondrial
Molecular weight formula_weight	45583.1 kDa
EC 编号 ec_number	2.6.1.1,2.6.1.7
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	12580

Recombinant expression, purification and preliminary crystallographic studies of the mature form of human mitochondrial aspartate aminotransferase

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

Aspartate aminotransferase, mitochondrial

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (1)

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

fit	/app/data/saxs_computation/ax/5ax8/5ax8.fit
pddf	/app/data/pr_computation/ax/5ax8/5ax8.pr.out
profile	/app/data/saxs_computation/ax/5ax8/5ax8.dat