SAXSdb — 7qc1

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

Proline--tRNA ligase

Plasmodium falciparum (isolate 3D7)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;[(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate ; × 1 1,2-ETHANEDIOL × 5 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	;[(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate ; × 1 1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	;[(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate ; × 1 1,2-ETHANEDIOL × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYP_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–504； UniProt 249–746 Author chain D； PDBConstruct 7–504； UniProt 249–746 Author chain I； PDBConstruct 7–504； UniProt 249–746

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	7qc1
Deposition date deposition_date	2021-11-22
Structure title title	Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436
Keywords keywords	Proline, Aminoacyl-tRNA synthetase, Ligase, Protein biosynthesis; 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.

7qc1__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7qc1__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7qc1__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.57 Å
Rg (electron density)	25.68 Å
Total Rg	26.45 Å
Atom count	3947
Residues	489
Excluded volume	70401 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7qc1__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7qc1__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`7qc1__assembly_3__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Proline--tRNA ligase
Molecular weight formula_weight	58526.9 kDa
EC 编号 ec_number	6.1.1.15
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,I
Atom count atom_count	11925

SDNAIASNILGITSKKIENFSDWYTQVIVKSELIEYYDISGCYILRPAAYYIWECVQAFFNKEIKKLNVENSYFPLFVTKNKLEKEKNHIEGFSPEVAWVTKYGDSNLPEEIAIRPTSETIMYSVFPKWIRSYRDLPLKLNQWNTVVRWEFKQPTPFIRTREFLWQEGHTAHKNEEEAVKLVFDILDLYRRWYEEYLAVPIIKGIKSEGEKFGGANFTSTAEAFISENGRAIQAATSHYLGTNFAKMFKIEFEDENEVKQYVHQTSWGCTTRSIGIMIMTHGDDKGLVLPPNVSKYKVVIVPIFYKTTDENAIHSYCKDIEKILKNAQINCVYDDRASYSPGYKFNHWELRGIPIRIEVGPKDLQNNSCVIVRRDNNEKCNVKKESVLLETQQMLVDIHKNLFLKAKKKLDDSIVQVTSFSEVMNALNKKKMVLAPWCEDIATEEEIKKETQRLSLNQTNSETTLSGAMKPLCIPLDQPPMPPNMKCFWSGKPAKRWCLFGRSY

Source Source

Source organism organism	Plasmodium falciparum (isolate 3D7)
NCBI taxonomy ID ncbi_taxonomy_id	36329
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;[(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate ;
Molecular weight formula_weight	886.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	73

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Unit-cell length a length_a	207.210 Å
Unit-cell length b length_b	207.210 Å
Unit-cell length c length_c	115.850 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.510 Å
Low-resolution limit resolution_low	65.530 Å
R factor r_factor	0.1935
R_work r_work	0.1914
R_free r_free	0.2333

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436

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

Proline--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

7qc1__assembly_2__model_1

7qc1__assembly_2__model_1 | I(q)

7qc1__assembly_2__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 (4)

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 water

7. Citations (1)

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436

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

Proline--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

7qc1__assembly_2__model_1

7qc1__assembly_2__model_1 | I(q)

7qc1__assembly_2__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 (4)

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 water

7. Citations (1)