SAXSdb — 6hhx

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

Aspartate--tRNA(Asp) ligase

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	5'-O-(N-(L-aspartyl)-sulfamoyl)cytidine × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYD_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–581； UniProt 1–580 Author chain B； PDBConstruct 2–581； UniProt 1–580

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	6hhx
Deposition date deposition_date	2018-08-29
Structure title title	Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)cytidine
Keywords keywords	protein-inhibitor complex, tRNA aminoacylation, 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.

6hhx__assembly_1__model_1

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

Download this curve (.dat)

6hhx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hhx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.90 Å
Rg (electron density)	34.42 Å
Total Rg	34.80 Å
Atom count	9051
Residues	1154
Excluded volume	160740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hhx__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Aspartate--tRNA(Asp) ligase
Molecular weight formula_weight	66181.8 kDa
EC 编号 ec_number	6.1.1.12
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	9213

GMRRTHYAGSLRETHVGEEVVLEGWVNRRRDLGGLIFLDLRDREGLVQLVAHPASPAYATAERVRPEWVVRAKGLVRLRPEPNPRLATGRVEVELSALEVLAEAKTPPFPVDAGWRGEEEKEASEELRLKYRYLDLRRRRMQENLRLRHRVIKAIWDFLDREGFVQVETPFLTKSTPEGARDFLVPYRHEPGLFYALPQSPQLFKQMLMVAGLDRYFQIARCFRDEDLRADRQPDFTQLDLEMSFVEVEDVLELNERLMAHVFREALGVELPLPFPRLSYEEAMERYGSDKPDLRFGLELKEVGPLFRQSGFRVFQEAESVKALALPKALSRKEVAELEEVAKRHKAQGLAWARVEEGGFSGGVAKFLEPVREALLQATEARPGDTLLFVAGPRKVAATALGAVRLRAADLLGLKREGFRFLWVVDFPLLEWDEEEEAWTYMHHPFTSPHPEDLPLLEKDPGRVRALAYDLVLNGVEVGGGSIRIHDPRLQARVFRLLGIGEEEQREKFGFFLEALEYGAPPHGGIAWGLDRLLALMTGSPSIREVIAFPKNKEGKDPLTGAPSPVPEEQLRELGLMVVRP

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	5'-O-(N-(L-aspartyl)-sulfamoyl)cytidine
Molecular weight formula_weight	437.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	162

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	6hhxA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	6hhxA02
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	6hhxB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	6hhxB02
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	82.123 Å
Unit-cell length b length_b	112.706 Å
Unit-cell length c length_c	88.679 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	57.780 Å
R factor r_factor	0.1888
R_work r_work	0.1881
R_free r_free	0.2178

Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)cytidine

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

Aspartate--tRNA(Asp) 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

6hhx__assembly_1__model_1

6hhx__assembly_1__model_1 | I(q)

6hhx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of T. thermophilus AspRS in Complex with 5'-O-(N-(L-aspartyl)-sulfamoyl)cytidine

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

Aspartate--tRNA(Asp) 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

6hhx__assembly_1__model_1

6hhx__assembly_1__model_1 | I(q)

6hhx__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)