SAXSdb — 7zog

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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 ;8-[[4-[2-[2-[2-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]sulfonylamino]-~{N}-(cyclohexylmethyl)-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide ; × 2 GLYCEROL × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	LYSINE × 2 ;8-[[4-[2-[2-[2-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]sulfonylamino]-~{N}-(cyclohexylmethyl)-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide ; × 2 GLYCEROL × 3 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 Author chain C； PDBConstruct 22–535； UniProt 46–559 Author chain D； 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	7zog
Deposition date deposition_date	2022-04-25
Structure title title	Crystal structure of Cryptosporidium parvum -Plasmodium falciparum mutant lysyl tRNA synthetase in complex with inhibitor
Keywords keywords	tRNA binding, 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.

7zog__assembly_1__model_1

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

Download this curve (.dat)

7zog__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zog__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.76 Å
Rg (electron density)	31.91 Å
Total Rg	32.57 Å
Atom count	8180
Residues	993
Excluded volume	146370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zog__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7zog__assembly_2__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	61464.1 kDa
EC 编号 ec_number	6.1.1.6
Mutation mutation	P272T, N293V, A309S
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17759

MAHHHHHHMGTLEAQTQGPGSHYTDNRYKMMECIKDAGRPFYPHKFKISMSLPAYALKYGNVENGYIDKDTTLSLSGRVTSIRSSSSKLIFYDIFCEEQKVQIIANIMEHDISTGEFSVSHSEIRRGDVVGFTGFPGKSKRGELSLFSKSVVLLSPCYHMLPTAISGLKDQEVRYRQRYLDLMLNEESRKVFKLRSRAIKYIRNYFDRLGFLEVETPMLNMIYGGAAARPFITYHNELETQLYMRIATELYLKQLIVGGLDKVYEIGKVFRNEGIDLTHNPEFTSMEFYMAYADYYDLMDLTEELISGLVLEIHGSLKIPYHPDGPEGKCIEIDFTTPWKRFSFVEEIESGLGEKLKRPLDSQENIDFMVEMCEKHEIELPHPRTAAKLLDKLAGHFVETKCTNPSFIIDHPQTMSPLAKWHREKPEMTERFELFVLGKELCNAYTELNEPLQQRKFFEQQADAKASGDVEACPIDETFCLALEHGLPPTGGWGLGIDRLIMFLADKNNIKEVILFPAMRNVKQNAQHSNQHSGN

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	4

Entity 3 Entity 3 non-polymer

Description description	;8-[[4-[2-[2-[2-[2-[(azanylidene-$l^{4}-azanylidene)amino]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]sulfonylamino]-~{N}-(cyclohexylmethyl)-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide ;
Molecular weight formula_weight	703.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1465

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7zogA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	7zogB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	7zogC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	7zogD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

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Unit-cell length a length_a	73.103 Å
Unit-cell length b length_b	118.732 Å
Unit-cell length c length_c	143.454 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	64.900 Å
R factor r_factor	0.1830
R_work r_work	0.1820
R_free r_free	0.2100

Crystal structure of Cryptosporidium parvum -Plasmodium falciparum mutant lysyl tRNA synthetase in complex with inhibitor

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

7zog__assembly_1__model_1

7zog__assembly_1__model_1 | I(q)

7zog__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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Cryptosporidium parvum -Plasmodium falciparum mutant lysyl tRNA synthetase in complex with inhibitor

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

7zog__assembly_1__model_1

7zog__assembly_1__model_1 | I(q)

7zog__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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)