SAXSdb — 7d5c

▼

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

Isoleucine--tRNA ligase, cytoplasmic

Saccharomyces cerevisiae S288c

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	;(2E,4S,5S,6E,8E)-10-[(2S,3R,6S,8R,9S)-3-butyl-9-methyl-2-[(1E,3E)-3-methyl-5-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-3-(4-oxidanyl-4-oxidanylidene-butanoyl)oxy-1,7-dioxaspiro[5.5]undecan-8-yl]-4,8-dimethyl-5-oxidanyl-deca-2,6,8-trienoic acid ; × 1 ;[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S,3S)-2-azanyl-3-methyl-pentanoate ; × 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	SYIC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–984； UniProt 1–984

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7d5c
Deposition date deposition_date	2020-09-25
Structure title title	IleRS in complex with a tRNA site inhibitor
Keywords keywords	tRNA synthetase, ligase-inhibitor complex; LIGASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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.

7d5c__assembly_1__model_1

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

Download this curve (.dat)

7d5c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7d5c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.94 Å
Rg (electron density)	36.80 Å
Total Rg	37.23 Å
Atom count	7538
Residues	919
Excluded volume	134890 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7d5c__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Isoleucine--tRNA ligase, cytoplasmic
Molecular weight formula_weight	114106.9 kDa
EC 编号 ec_number	6.1.1.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8273

MSESNAHFSFPKEEEKVLSLWDEIDAFHTSLELTKDKPEFSFFDGPPFATGTPHYGHILASTIKDIVPRYATMTGHHVERRFGWDTHGVPIEHIIDKKLGITGKDDVFKYGLENYNNECRSIVMTYASDWRKTIGRLGRWIDFDNDYKTMYPSFMESTWWAFKQLHEKGQVYRGFKVMPYSTGLTTPLSNFEAQQNYKDVNDPAVTIGFNVIGQEKTQLVAWTTTPWTLPSNLSLCVNADFEYVKIYDETRDRYFILLESLIKTLYKKPKNEKYKIVEKIKGSDLVGLKYEPLFPYFAEQFHETAFRVISDDYVTSDSGTGIVHNAPAFGEEDNAACLKNGVISEDSVLPNAIDDLGRFTKDVPDFEGVYVKDADKLIIKYLTNTGNLLLASQIRHSYPFCWRSDTPLLYRSVPAWFVRVKNIVPQMLDSVMKSHWVPNTIKEKRFANWIANARDWNVSRNRYWGTPIPLWVSDDFEEVVCVGSIKELEELTGVRNITDLHRDVIDKLTIPSKQGKGDLKRIEEVFDCWFESGSMPYASQHYPFENTEKFDERVPANFISEGLDQTRGWFYTLAVLGTHLFGSVPYKNVIVSGIVLAADGRKMSKSLKNYPDPSIVLNKYGADALRLYLINSPVLKAESLKFKEEGVKEVVSKVLLPWWNSFKFLDGQIALLKKMSNIDFQYDDSVKSDNVMDRWILASMQSLVQFIHEEMGQYKLYTVVPKLLNFIDELTNWYIRFNRRRLKGENGVEDCLKALNSLFDALFTFVRAMAPFTPFLSESIYLRLKEYIPEAVLAKYGKDGRSVHFLSYPVVKKEYFDEAIETAVSRMQSVIDLGRNIREKKTISLKTPLKTLVILHSDESYLKDVEALKNYIIEELNVRDVVITSDEAKYGVEYKAVADWPVLGKKLKKDAKKVKDALPSVTSEQVREYLESGKLEVAGIELVKGDLNAIRGLPESAVQAGQETRTDQDVLIIMDTNIYSELKSLEHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(2E,4S,5S,6E,8E)-10-[(2S,3R,6S,8R,9S)-3-butyl-9-methyl-2-[(1E,3E)-3-methyl-5-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-3-(4-oxidanyl-4-oxidanylidene-butanoyl)oxy-1,7-dioxaspiro[5.5]undecan-8-yl]-4,8-dimethyl-5-oxidanyl-deca-2,6,8-trienoic acid ;
Molecular weight formula_weight	660.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	;[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S,3S)-2-azanyl-3-methyl-pentanoate ;
Molecular weight formula_weight	460.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	673

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7d5cA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	730 — Isoleucyl-tRNA Synthetase; Domain 1
Homologous superfamily homologous superfamily	10 — Isoleucyl-tRNA Synthetase; Domain 1

▶

Unit-cell length a length_a	170.649 Å
Unit-cell length b length_b	64.758 Å
Unit-cell length c length_c	142.229 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.895 Å
Low-resolution limit resolution_low	41.580 Å
R factor r_factor	0.1775
R_work r_work	0.1766
R_free r_free	0.1943

IleRS in complex with a tRNA site inhibitor

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

Isoleucine--tRNA ligase, cytoplasmic

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

7d5c__assembly_1__model_1

7d5c__assembly_1__model_1 | I(q)

7d5c__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

IleRS in complex with a tRNA site inhibitor

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

Isoleucine--tRNA ligase, cytoplasmic

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

7d5c__assembly_1__model_1

7d5c__assembly_1__model_1 | I(q)

7d5c__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)