SAXSdb — 5ifu

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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	5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide × 1 CHLORIDE ION × 1 FORMIC ACID × 10 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide × 1 FORMIC ACID × 4 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide × 4 CHLORIDE ION × 2 FORMIC ACID × 28 1,2-ETHANEDIOL × 4 water × 4	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 9–506； UniProt 249–746 Author chain B； PDBConstruct 9–506； 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	5ifu
Deposition date deposition_date	2016-02-26
Structure title title	Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Glyburide
Keywords keywords	;Plasmodium falciparum, Prolyl-tRNA synthetase, ProRS, Proline--tRNA ligase, Glyburide, Structural Genomics, Structural Genomics Consortium, SGC, 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.

5ifu__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5ifu__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ifu__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	41.38 Å
Rg (electron density)	40.60 Å
Total Rg	41.10 Å
Atom count	14092
Residues	1766
Excluded volume	251000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ifu__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5ifu__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5ifu__assembly_3__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Proline--tRNA ligase
Molecular weight formula_weight	58986.5 kDa
EC 编号 ec_number	6.1.1.15
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	7313

MAHHHHHHSNILGITSKKIENFSDWYTQVIVKSELIEYYDISGCYILRPAAYYIWECVQAFFNKEIKKLNVENSYFPLFVTKNKLEKEKNHIEGFSPEVAWVTKYGDSNLPEEIAIRPTSETIMYSVFPKWIRSYRDLPLKLNQWNTVVRWEFKQPTPFIRTREFLWQEGHTAHKNEEEAVKLVFDILDLYRRWYEEYLAVPIIKGIKSEGEKFGGANFTSTAEAFISENGRAIQAATSHYLGTNFAKMFKIEFEDENEVKQYVHQTSWGCTTRSIGIMIMTHGDDKGLVLPPNVSKYKVVIVPIFYKTTDENAIHSYCKDIEKILKNAQINCVYDDRASYSPGYKFNHWELRGIPIRIEVGPKDLQNNSCVIVRRDNNEKCNVKKESVLLETQQMLVDIHKNLFLKAKKKLDDSIVQVTSFSEVMNALNKKKMVLAPWCEDIATEEEIKKETQRLSLNQTNSETTLSGAMKPLCIPLDQPPMPPNMKCFWSGKPAKRWCLFGRSY

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide
Molecular weight formula_weight	494.0 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	1

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	243

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5ifuA01
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	5ifuA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	5ifuA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

Domain ID domain_id	5ifuB01
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	5ifuB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	5ifuB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

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Unit-cell length a length_a	138.310 Å
Unit-cell length b length_b	138.310 Å
Unit-cell length c length_c	156.660 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	16

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

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	43.737 Å
R factor r_factor	0.1863
R_work r_work	0.1850
R_free r_free	0.2129

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

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

5ifu__assembly_3__model_1

5ifu__assembly_3__model_1 | I(q)

5ifu__assembly_3__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

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

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

5ifu__assembly_3__model_1

5ifu__assembly_3__model_1 | I(q)

5ifu__assembly_3__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 (6)

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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)