SAXSdb — 1akb

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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	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 experimental conditions	Resolution 2.30 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 1AKB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AKA 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） Chain B 23–423（401 aa）	Mutation：K272H Mutation：K272H	PLP PYRIDOXAL-5'-PHOSPHATE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 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 mutation/modification Different ligand/ion	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 mutation/modification Different ligand/ion	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 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 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 mutation/modification Different ligand/ion	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 construct Different mutation/modification Different ligand/ion	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 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 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） 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 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） 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 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） 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 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） 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 construct Different mutation/modification Different ligand/ion	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 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） 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

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	1akb
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	22.94 Å
Radius of gyration Rg (electron density) rg_electron	21.87 Å
Forward intensity I(0) i0	35157900.00
Molecular weight molecular_weight	45313.0 kDa
Excluded volume excluded_volume	56639 Å³
Envelope volume envelope_volume	68531 Å³
Hydration-shell volume shell_volume	25705 Å³
Envelope diameter envelope_diameter	71.4 Å
Shell Rg shell_rg	29.06 Å
Envelope Rg envelope_rg	22.26 Å
Shape Rg shape_rg	21.85 Å
Total Rg total_rg	22.82 Å
Total atoms total_atoms	3186
Residues n_residues	401
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	70.0 Å
Rg (real space) rg_real	22.83 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	3.5160e+07
I(0) uncertainty (real space) i0_real_error	4.3120e+05
Rg (reciprocal space) rg_reciprocal	22.86 Å
I(0) (reciprocal space) i0_reciprocal	35160000.0000
Solution quality estimate total_estimate	0.9095
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.0 Å
Skewness Skewness skewness	0.193
Kurtosis Kurtosis kurtosis	-0.483
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7428000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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	K250H
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3498

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	2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYLENE)-AMINO]-SUCCINIC ACID
Molecular weight formula_weight	364.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	312

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1akba_
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 (2 domains)

Domain ID domain_id	1akbA01
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	1akbA02
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	70.100 Å
Unit-cell length b length_b	91.800 Å
Unit-cell length c length_c	129.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1780
R_work r_work	—
R_free r_free	—

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

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

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

ASPARTATE AMINOTRANSFERASE

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