SAXSdb — 9r3f

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

Lysine--tRNA ligase

Cryptosporidium parvum Iowa II

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	LYSINE × 2 ;2-azanyl-6-[[(1~{R},3~{S})-1-(2-azanylethyl)-3-(trifluoromethyl)cyclohexyl]methyl]-4-(trifluoromethyl)-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one ; × 2 SULFATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5CR27_CRYPI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–535； UniProt 46–559 Author chain B； PDBConstruct 22–535； UniProt 46–559

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	9r3f
Deposition date deposition_date	2025-05-05
Last revision last_revision	2026-06-10
Structure title title	CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01932549
Keywords keywords	inhibitor, LIGASE; LIGASE
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.

9r3f__assembly_1__model_1

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

Download this curve (.dat)

9r3f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9r3f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.74 Å
Rg (electron density)	31.98 Å
Total Rg	32.64 Å
Atom count	8136
Residues	995
Excluded volume	145260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9r3f__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	Lysine--tRNA ligase
Molecular weight formula_weight	61459.1 kDa
EC 编号 ec_number	6.1.1.6
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	8936

MAHHHHHHMGTLEAQTQGPGSHYTDNRYKMMECIKDAGRPFYPHKFKISMSLPAYALKYGNVENGYIDKDTTLSLSGRVTSIRSSSSKLIFYDIFCEEQKVQIIANIMEHDISTGEFSVSHSEIRRGDVVGFTGFPGKSKRGELSLFSKSVVLLSPCYHMLPTAISGLKDQEVRYRQRYLDLMLNEESRKVFKLRSRAIKYIRNYFDRLGFLEVETPMLNMIYGGAAARPFITYHNELETQLYMRIAPELYLKQLIVGGLDKVYEIGKNFRNEGIDLTHNPEFTAMEFYMAYADYYDLMDLTEELISGLVLEIHGSLKIPYHPDGPEGKCIEIDFTTPWKRFSFVEEIESGLGEKLKRPLDSQENIDFMVEMCEKHEIELPHPRTAAKLLDKLAGHFVETKCTNPSFIIDHPQTMSPLAKWHREKPEMTERFELFVLGKELCNAYTELNEPLQQRKFFEQQADAKASGDVEACPIDETFCLALEHGLPPTGGWGLGIDRLIMFLADKNNIKEVILFPAMRNVKQNAQHSNQHSGN

Source Source

Source organism organism	Cryptosporidium parvum Iowa II
NCBI taxonomy ID ncbi_taxonomy_id	353152
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	LYSINE
Molecular weight formula_weight	147.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	;2-azanyl-6-[[(1~{R},3~{S})-1-(2-azanylethyl)-3-(trifluoromethyl)cyclohexyl]methyl]-4-(trifluoromethyl)-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one ;
Molecular weight formula_weight	425.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	796

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Unit-cell length a length_a	73.152 Å
Unit-cell length b length_b	116.852 Å
Unit-cell length c length_c	143.262 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	P 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	46.924 Å
R factor r_factor	—
R_work r_work	0.2137
R_free r_free	0.2612

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01932549

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

Lysine--tRNA ligase

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

9r3f__assembly_1__model_1

9r3f__assembly_1__model_1 | I(q)

9r3f__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)

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Cryptosporidium parvum COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01932549

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

Lysine--tRNA ligase

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

9r3f__assembly_1__model_1

9r3f__assembly_1__model_1 | I(q)

9r3f__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)