SAXSdb — 2v0c

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

AMINOACYL-TRNA SYNTHETASE

THERMUS THERMOPHILUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	LEUCINE × 1 [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE × 1 ZINC ION × 2 ;[(6-AMINO-9H-PURIN-9-YL)-[5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1-BENZOXABOROLE]-4'YL]METHYL DIHYDROGEN PHOSPHATE ; × 1 SULFATE ION × 5 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7SIE4_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–878； UniProt 1–878

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	2v0c
Deposition date deposition_date	2007-05-14
Structure title title	LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE In the synthetic site and an adduct of AMP with 5-Fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (AN2690) in the editing site
Keywords keywords	;LIGASE, NUCLEOTIDE-BINDING, PROTEIN BIOSYNTHESIS, CLSS I AMINOACYL- TRNA SYNTHETASE, ATP + L-LEUCINE + TRNA (LEU) GIVES AMP + PPI + L-LEUCYL-TRNA(LEU), AMINOACYL-TRNA SYNTHETASE, ZINC, ATP-BINDING, METAL-BINDING ;; 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.

2v0c__assembly_1__model_1

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

Download this curve (.dat)

2v0c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v0c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.17 Å
Rg (electron density)	32.67 Å
Total Rg	33.16 Å
Atom count	6699
Residues	810
Excluded volume	119200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v0c__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	AMINOACYL-TRNA SYNTHETASE
Molecular weight formula_weight	100997.9 kDa
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	7383

MEKYNPHAIEAKWQRFWEEKGFMKAKDLPGGRGKQYVLVMFPYPSGDLHMGHLKNYTMGDVLARFRRMQGYEVLHPMGWDAFGLPAENAALKFGVHPKDWTYANIRQAKESLRLMGILYDWDREVTTCEPEYYRWNQWIFLKMWEKGLAYRAKGLVNWCPKCQTVLANEQVVEGRCWRHEDTPVEKRELEQWYLRITAYAERLLKDLEGLNWPEKVKAMQRAWIGRSEGAEILFPVEGKEVRIPVFTTRPDTLFGATFLVLAPEHPLTLELAAPEKREEVLAYVEAAKRKTEIERQAEGREKTGVFLGAYALNPATGERIPIWTADYVLFGYGTGAIMAVPAHDQRDYEFARKFGLPIKKVIERPGEPLPEPLERAYEEPGIMVNSGPFDGTESEEGKRKVIAWLEEKGLGKGRVTYRLRDWLISRQRYWGTPIPMVHCEACGVVPVPEEELPVLLPDLKDVEDIRPKGKSPLEAHPEFYETTCPKCGGPAKRDTDTMDTFFDSSWYYLRYTDPHNDRLPFDPEKANAWMPVDQYIGGVEHAVLHLLYSRFFTKFLHDLGMVKVEEPFQGLFTQGMVLAWTDFGPVEVEGSVVRLPEPTRIRLEIPESALSLEDVRKMGAELRPHEDGTLHLWKPAVMSKSKGNGVMVGPFVKEQGADIARITILFAAPPENEMVWTEEGVQGAWRFLNRIYRRVAEDREALLETSGVFQAEALEGKDRELYGKLHETLKKVTEDLEALRFNTAIAALMEFLNALYEYRKDRPVTPVYRTAIRYYLQMLFPFAPHLAEELWHWFWPDSLFEAGWPELDEKALEKDVVEVAVQVNGAVAGTIHIPKDAPLEVARAEALKVRNVRAHLEGKEVVKEIYVPGKILNLVVRG

Source Source

Source organism organism	THERMUS THERMOPHILUS
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	LEUCINE
Molecular weight formula_weight	131.2 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-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDRO-2-FURANYL]METHYL SULFAMATE
Molecular weight formula_weight	346.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	;[(6-AMINO-9H-PURIN-9-YL)-[5-FLUORO-1,3-DIHYDRO-1-HYDROXY-2,1-BENZOXABOROLE]-4'YL]METHYL DIHYDROGEN PHOSPHATE ;
Molecular weight formula_weight	480.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	684

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2v0cA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	2v0cA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	740 — Isoleucyl-tRNA Synthetase; domain 2
Homologous superfamily homologous superfamily	10 — Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain

Domain ID domain_id	2v0cA03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	210 — Leucyl-tRNA synthetase, domain 3
Homologous superfamily homologous superfamily	10 — Leucyl-tRNA synthetase, domain 3

Domain ID domain_id	2v0cA04
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

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Unit-cell length a length_a	101.830 Å
Unit-cell length b length_b	154.230 Å
Unit-cell length c length_c	174.950 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	87.370 Å
R factor r_factor	0.1810
R_work r_work	0.1800
R_free r_free	0.2020

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE In the synthetic site and an adduct of AMP with 5-Fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (AN2690) in the editing site

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

AMINOACYL-TRNA SYNTHETASE

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

2v0c__assembly_1__model_1

2v0c__assembly_1__model_1 | I(q)

2v0c__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE In the synthetic site and an adduct of AMP with 5-Fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole (AN2690) in the editing site

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

AMINOACYL-TRNA SYNTHETASE

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

2v0c__assembly_1__model_1

2v0c__assembly_1__model_1 | I(q)

2v0c__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)