SAXSdb — 12pl

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

Serine/threonine protein kinase, putative

Trypanosoma cruzi

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 123–474 Chain B； UniProt 123–474	Fragment：residues 123-474 Mutation：T185I, V227F, N314S Non-standard monomer：Yes (specific site not provided by mmCIF)	LMS [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；3.0M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. Cocrystallization with 4mM ATP and 4mM MgCl2. Crystals were soaked overnight in 10 mM LMS solubilized in 3.0M Malonate, pH 5.0 (cryo solution) which displaced the ATP. plate Liu-S-198, Puck: PSL-0206, Cryo: 3.0M Sodium Malonate	Resolution 2.82 Å R-free 0.279

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 12PL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10BL Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex ADP Deposited 2026-01-09	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 123–474（352 aa） Fragment：residues 123-474 Chain B 123–474（352 aa） Fragment：residues 123-474	Mutation：T185I, V227F, N314S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：T185I, V227F, N314S Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Grid Salt Screen, C12: 3.40M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. 4mM ATP and 4mM MgCl2 added to the protein prior to crystallization but only ADP was bound. several Ser residues displayed electron density consistent with phosphorylation. plate 20528 C12, Puck: PSL-0916, Cryo: 2.5M LiSO4	Resolution 2.60 Å R-free 0.265
10SL Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with Hesperadin Deposited 2026-02-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 123–474（352 aa） Fragment：residues 123-474 Chain B 123–474（352 aa） Fragment：residues 123-474	Mutation：T185I, V227F, N314S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：T185I, V227F, N314S Non-standard monomer：Yes (specific site not provided by mmCIF)	H1N N-[2-OXO-3-((E)-PHENYL{[4-(PIPERIDIN-1-YLMETHYL)PHENYL]IMINO}METHYL)-2,6-DIHYDRO-1H-INDOL-5-YL]ETHANESULFONAMIDE × 2 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；3.0M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. Cocrystallization with 4mM ATP and 4mM MgCl2. Crystals were soaked overnight in 10 mM Hespreadin solubilized in 3.0M Malonate, pH 5.0 which displaced the ATP. plate Liu-S-198, Puck: PSL-1705, Cryo: 3.0M Sodium Malonate	Resolution 2.72 Å R-free 0.269
12OB Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with AMP Deposited 2026-04-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 123–474（352 aa） Fragment：residues 123-474 Chain B 123–474（352 aa） Fragment：residues 123-474	Mutation：T185I, V227F, N314S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：T185I, V227F, N314S Non-standard monomer：Yes (specific site not provided by mmCIF)	AMP ADENOSINE MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；3.0M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. Cocrystallization with 4mM ATP and 4mM MgCl2. Crystals were soaked overnight in 10 mM AMP solubilized in 3.0M Malonate, pH 5.0 (cryo solution) which displaced the ATP. plate Liu-S-198, Puck: PSL-0201, Cryo: 3.0M Sodium Malonate	Resolution 2.83 Å R-free 0.281
12OC Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with ATP Deposited 2026-04-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 123–474（352 aa） Fragment：residues 123-474 Chain B 123–474（352 aa） Fragment：residues 123-474	Mutation：T185I, V227F, N314S Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：T185I, V227F, N314S Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；3.0M Sodium Malonate, pH 5.0. TrcrB.01480.a.WW4.PS38791 at 16.9 mg/mL. Cocrystallization with 4mM ATP and 4mM MgCl2. Crystals were soaked overnight in 10 mM ATP solubilized in 3.0M Malonate, pH 5.0 (cryo solution) which displaced the ATP. plate Liu-S-198, Puck: PSL-0203, Cryo: 3.0M Sodium Malonate	Resolution 2.68 Å R-free 0.283

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q4E2L0_TRYCC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–353； UniProt 123–474 Author chain B； PDBConstruct 2–353； UniProt 123–474

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	12pl
Deposition date deposition_date	2026-04-14
最后修订 last_revision	2026-04-22
Structure title title	Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with LMS
Keywords keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, serine/threonine-protein kinase, TRANSFERASE ;; TRANSFERASE
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	27.31 Å
Radius of gyration Rg (electron density) rg_electron	26.36 Å
Forward intensity I(0) i0	83264200.00
Molecular weight molecular_weight	72521.0 kDa
Excluded volume excluded_volume	91068 Å³
Envelope volume envelope_volume	112840 Å³
Hydration-shell volume shell_volume	35005 Å³
Envelope diameter envelope_diameter	89.1 Å
Shell Rg shell_rg	34.52 Å
Envelope Rg envelope_rg	26.50 Å
Shape Rg shape_rg	26.37 Å
Total Rg total_rg	27.21 Å
Total atoms total_atoms	5117
Residues n_residues	640
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	85.6 Å
Rg (real space) rg_real	27.21 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	8.3260e+07
I(0) uncertainty (real space) i0_real_error	1.2320e+06
Rg (reciprocal space) rg_reciprocal	27.24 Å
I(0) (reciprocal space) i0_reciprocal	83270000.0000
Solution quality estimate total_estimate	0.8993
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	84.1 Å
Skewness Skewness skewness	0.265
Kurtosis Kurtosis kurtosis	-0.377
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23730000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Serine/threonine protein kinase, putative
Molecular weight formula_weight	41649.3 kDa
Mutation mutation	T185I, V227F, N314S
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	5117

MEKVTKDDFESLDVLGKGSFAYVVLVRRIGTNEYYAMKVVNKQGLLDHNRYRDVFVERNVLSRINHPYLLKLYWTFQSEHKLFFVMEYMPGGDLDKYMNNLPSKQFDLFTAKLYAAEILLALLFLHEHSVIYRDLKPENILLTGDGHCVLADFGLSKDFYNPKEGGDASTKDMRANSFVGSPFYVAPDVLKQSEYTNAVDFWSFGILLYRMLCGRTPFNGKSMREVFDNILYSDLRFPSSVQLPSEAKDLISRLLIKDANRRIKGPEIKAHLFWTGINFDEVMERKVKPPKWVPIPSPEQVMAERAKAEGASTSAKNPGQLVNTPAQSSQLNSRQQQLFTGFSCTADNHLNKNLEHHHHHH

来源 Source

来源生物 organism	Trypanosoma cruzi
NCBI Class编号 ncbi_taxonomy_id	5693
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE
Molecular weight formula_weight	346.3 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	86.193 Å
Unit-cell length b length_b	86.193 Å
Unit-cell length c length_c	193.256 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.820 Å
Low-resolution limit resolution_low	48.770 Å
R factor r_factor	0.2422
R_work r_work	0.2401
R_free r_free	0.2793

fit	/app/data/saxs_computation/2p/12pl/12pl.fit
pddf	/app/data/pr_computation/2p/12pl/12pl.pr.out
profile	/app/data/saxs_computation/2p/12pl/12pl.dat

Crystal Structure of serine/threonine-protein kinase (AEK1) from Trypanosoma cruzi in complex with LMS

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

Serine/threonine protein kinase, putative

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 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)