SAXSdb — 1aka

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

ASPARTATE AMINOTRANSFERASE

Gallus gallus

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 23–423 Chain B； UniProt 23–423	Mutation：K272H	PLP PYRIDOXAL-5'-PHOSPHATE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.10 Å

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 1AKA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AKB STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRANSFERASE K258H LACKING ITS PYRIDOXAL-5'-PHOSPHATE-BINDING LYSINE RESIDUE Deposited 1994-02-28	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa）	Mutation：K250H	PPD 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYLENE)-AMINO]-SUCCINIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1AKC Structural basis for the catalytic activity of aspartate aminotransferase K258H lacking its pyridoxal-5'-phosphate-binding lysine residue Deposited 1994-02-28	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa）	Not recorded	PPE 4-[(1,3-DICARBOXY-PROPYLAMINO)-METHYL]-3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDINIUM × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1AMA DOMAIN CLOSURE IN MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE Deposited 1992-02-05	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa）	Not recorded	PLA 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1IVR STRUCTURE OF ASPARTATE AMINOTRANSFERASE Deposited 1996-10-11	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa）	Not recorded	CBA N-PYRIDOXYL-2,3-DIHYDROXYASPARTIC ACID-5-MONOPHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1MAP CRYSTAL STRUCTURES OF TRUE ENZYMATIC REACTION INTERMEDIATES: ASPARTATE AND GLUTAMATE KETIMINES IN ASPARTATE AMINOTRANSFERASE Deposited 1993-09-10	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa）	Not recorded	KET 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYLENE)-AMINO]-SUCCINIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1MAQ CRYSTAL STRUCTURES OF TRUE ENZYMATIC REACTION INTERMEDIATES: ASPARTATE AND GLUTAMATE KETIMINES IN ASPARTATE AMINOTRANSFERASE Deposited 1993-09-10	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa）	Not recorded	PGU N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-glutamic acid × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1OXO ASPARTATE AMINOTRANSFERASE, H-ASP COMPLEX, OPEN CONFORMATION Deposited 1995-12-23	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa） Chain B 23–423（401 aa）	Not recorded	IK2 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1OXP ASPARTATE AMINOTRANSFERASE, H-ASP COMPLEX, CLOSED CONFORMATION Deposited 1995-12-23	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa）	Not recorded	IK2 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
1TAR CRYSTALLINE MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE EXISTS IN ONLY TWO CONFORMATIONS Deposited 1993-10-04	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa） Chain B 23–423（401 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1TAS CRYSTALLINE MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE EXISTS IN ONLY TWO CONFORMATIONS Deposited 1993-10-04	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa） Chain B 23–423（401 aa）	Not recorded	PLA 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1TAT CRYSTALLINE MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE EXISTS IN ONLY TWO CONFORMATIONS Deposited 1993-10-04	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa） Chain B 23–423（401 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
7AAT X-RAY STRUCTURE REFINEMENT AND COMPARISON OF THREE FORMS OF MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE Deposited 1991-12-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa） Chain B 23–423（401 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
8AAT X-RAY STRUCTURE REFINEMENT AND COMPARISON OF THREE FORMS OF MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE Deposited 1991-12-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa） Chain B 23–423（401 aa）	Not recorded	PLP PYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
9AAT X-RAY STRUCTURE REFINEMENT AND COMPARISON OF THREE FORMS OF MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE Deposited 1991-12-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–423（401 aa） Chain B 23–423（401 aa）	Not recorded	PMP 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AATM_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–401； UniProt 23–423 Author chain B； PDBConstruct 1–401； UniProt 23–423

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	1aka
Deposition date deposition_date	1994-02-28
Structure title title	STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRANSFERASE K258H LACKING ITS PYRIDOXAL-5'-PHOSPHATE-BINDING LYSINE RESIDUE
Keywords keywords	TRANSFERASE(AMINOTRANSFERASE); TRANSFERASE(AMINOTRANSFERASE)
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	29.43 Å
Radius of gyration Rg (electron density) rg_electron	28.52 Å
Forward intensity I(0) i0	130870000.00
Molecular weight molecular_weight	90239.0 kDa
Excluded volume excluded_volume	112810 Å³
Envelope volume envelope_volume	135100 Å³
Hydration-shell volume shell_volume	39065 Å³
Envelope diameter envelope_diameter	103.1 Å
Shell Rg shell_rg	36.27 Å
Envelope Rg envelope_rg	28.62 Å
Shape Rg shape_rg	28.51 Å
Total Rg total_rg	29.25 Å
Total atoms total_atoms	6345
Residues n_residues	802
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	100.0 Å
Rg (real space) rg_real	29.41 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	1.3090e+08
I(0) uncertainty (real space) i0_real_error	2.0240e+06
Rg (reciprocal space) rg_reciprocal	29.42 Å
I(0) (reciprocal space) i0_reciprocal	130900000.0000
Solution quality estimate total_estimate	0.8766
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.365
Kurtosis Kurtosis kurtosis	-0.217
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	55260000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.968

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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	ASPARTATE AMINOTRANSFERASE
Molecular weight formula_weight	45001.5 kDa
EC 编号 ec_number	2.6.1.1
Mutation mutation	K272H
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	7011

SSWWSHVEMGPPDPILGVTEAFKRDTNSKKMNLGVGAYRDDNGKPYVLNCVRKAEAMIAAKKMDKEYLPIAGLADFTRASAELALGENSEAFKSGRYVTVQGISGTGSLRVGANFLQRFFKFSRDVYLPKPSWGNHTPIFRDAGLQLQAYRYYDPKTCSLDFTGAMEDISKIPEKSIILLHACAHNPTGVDPRQEQWKELASVVKKRNLLAYFDMAYQGFASGDINRDAWALRHFIEQGIDVVLSQSYAHNMGLYGERAGAFTVICRDAEEAKRVESQLKILIRPMYSNPPMNGARIASLILNTPELRKEWLVEVKGMADRIISMRTQLVSNLKKEGSSHNWQHITDQIGMFCFTGLKPEQVERLTKEFSIYMTKDGRISVAGVASSNVGYLAHAIHQVTK

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	unidentified

Entity 2 Entity 2 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	666

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1akaa_
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	d1akab_
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 (4 domains)

Domain ID domain_id	1akaA01
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	1akaA02
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	1akaB01
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	1akaB02
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)

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8. Citations (3)

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Unit-cell length a length_a	55.870 Å
Unit-cell length b length_b	58.800 Å
Unit-cell length c length_c	75.810 Å
Unit-cell angle α angle_alpha	85.26 °
Unit-cell angle β angle_beta	108.96 °
Unit-cell angle γ angle_gamma	115.57 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1690
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ak/1aka/1aka.fit
pddf	/app/data/pr_computation/ak/1aka/1aka.pr.out
profile	/app/data/saxs_computation/ak/1aka/1aka.dat

STRUCTURAL BASIS FOR THE CATALYTIC ACTIVITY OF ASPARTATE AMINOTRANSFERASE K258H LACKING ITS PYRIDOXAL-5'-PHOSPHATE-BINDING LYSINE RESIDUE