SAXSdb — 9d03

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

Threonine aspartase subunit beta,Threonine aspartase subunit alpha

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SODIUM ION × 2 CHLORIDE ION × 3 1-(ethenylsulfonyl)-4-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}piperazine × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TASP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–184； UniProt 234–416 Author chain A； PDBConstruct 189–331； UniProt 41–183 Author chain B； PDBConstruct 2–184； UniProt 234–416 Author chain B； PDBConstruct 189–331； UniProt 41–183

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	9d03
Deposition date deposition_date	2024-08-06
Last revision last_revision	2025-08-13
Structure title title	Co-crystal structure of circularly permuted human taspase-1 bound to ligand SMDC1014689 1-(ethenesulfonyl)-4-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}piperazine
Keywords keywords	MLL, TASPASE-1, CIRCULAR PERMUTATION, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9d03__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9d03__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9d03__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	24.49 Å
Rg (electron density)	23.52 Å
Total Rg	24.32 Å
Atom count	4368
Residues	621
Excluded volume	76694 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9d03__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Threonine aspartase subunit beta,Threonine aspartase subunit alpha
Molecular weight formula_weight	35344.0 kDa
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	4463

MTVGAVVVDHEGNVAAAVSSGGLALKHPGRVGQAALYGCGCWAENTGAHNPYSTAVSTSGCGEHLVRTILARECSHALQAEDAHQALLETMQNKFISSPFLASEDGVLGGVIVLRSCRCSAEPDSSQNKQTLLVEFLWSHTTESMCVGYMSAQDGKAKTHISRLPPGAVAGQSVAIEGGVCRLEGSGSGGFVLVHAGAGYHSESKAKEYKHVCKRACQKAIEKLQAGALATDAVTAALVELEDSPFTNAGMGSNLNLLGEIECDASIMDGKSLNFGAVGALSGIKNPVSVANRLLCEGQKGKLSAGRIPPCFLVGEGAYRWAVDHGIPSCPLEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	1-(ethenylsulfonyl)-4-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}piperazine
Molecular weight formula_weight	368.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	63

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Unit-cell length a length_a	60.330 Å
Unit-cell length b length_b	60.330 Å
Unit-cell length c length_c	316.670 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	46.830 Å
R factor r_factor	0.1620
R_work r_work	0.1590
R_free r_free	0.2010

Co-crystal structure of circularly permuted human taspase-1 bound to ligand SMDC1014689 1-(ethenesulfonyl)-4-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}piperazine

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

Threonine aspartase subunit beta,Threonine aspartase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9d03__assembly_1__model_1

9d03__assembly_1__model_1 | I(q)

9d03__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Co-crystal structure of circularly permuted human taspase-1 bound to ligand SMDC1014689 1-(ethenesulfonyl)-4-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}piperazine

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

Threonine aspartase subunit beta,Threonine aspartase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9d03__assembly_1__model_1

9d03__assembly_1__model_1 | I(q)

9d03__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)