SAXSdb — 3afh

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

Glutamyl-tRNA synthetase 2

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYE2_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–488； UniProt 2–487

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	3afh
Deposition date deposition_date	2010-03-01
Structure title title	Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with a glutamyl-AMP analog
Keywords keywords	;PROTEIN-SUBSTRATE COMPLEX, non-discriminating glutamyl-tRNA synthetase, Aminoacyl-tRNA synthetase, ATP-binding, Ligase, Nucleotide-binding, 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.

3afh__assembly_1__model_1

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

Download this curve (.dat)

3afh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3afh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.93 Å
Rg (electron density)	31.42 Å
Total Rg	31.71 Å
Atom count	3887
Residues	463
Excluded volume	69216 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	Glutamyl-tRNA synthetase 2
Molecular weight formula_weight	57525.6 kDa
EC 编号 ec_number	6.1.1.17
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	4403

MGFITGAFFDILEVGPKKIRRCFELVRVRFAPSPTGHLHVGGARTALFNWMFARKEGGKFILRIEDTDTERSSREYEQQILESLRWCGLDWDEGPDIGGDFGPYRQSERLEIYREYAEKLVEDKRAYYVVYDKEDPSKELFTTYEYPHEYKEKGHPVTIKFKVLPGKTSFEDLLKGYMEFDNSTLEDFIIMKSNGFPTYNFAVVVDDHLMRISHVFRGEDHLSNTPKQLMIYEAFGWEAPVFMHIPLILGSDRTPLSKRHGATSVEHFRREGILSRALMNYLALLGWRVEGDEIFTIEEKLQSFDPKDISNKGVIFDYQKLEWVNGKHMRRIDLEDLKREFIEWAKYAGKEIPSVDERYFSETLRICREKVNTLSQLYDIMYPFMNDDYEYEKDYVEKFLKREEAERVLEEAKKAFKDLNSWNMEEIEKTLRDLSEKGLASKKVVFQLIRGAVTGKLVTPGLFETIEVLGKERTLKRLERTLQFLKKT

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	O5'-(L-GLUTAMYL-SULFAMOYL)-ADENOSINE
Molecular weight formula_weight	475.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	516

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3afha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.0 — automated matches

Domain ID domain_id	d3afha2
Class class	a — All alpha proteins
Fold Fold fold	a.97 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases
Superfamily Superfamily superfamily	a.97.1 — An anticodon-binding domain of class I aminoacyl-tRNA synthetases
Family Family family	a.97.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	3afhA01
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	3afhA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	800 — Glutamyl-tRNA Synthetase; domain 3
Homologous superfamily homologous superfamily	10 — Glutamyl-tRNA Synthetase; Domain 3

Domain ID domain_id	3afhA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1160 — Glutamyl-tRNA Synthetase; domain 2
Homologous superfamily homologous superfamily	10 — Glutamyl-trna Synthetase; Domain 2

Domain ID domain_id	3afhA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	70 — Glutamate-tRNA synthetase, class I, anticodon-binding domain 1

Domain ID domain_id	3afhA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	350 —

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Unit-cell length a length_a	68.624 Å
Unit-cell length b length_b	207.317 Å
Unit-cell length c length_c	39.495 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	39.500 Å
R factor r_factor	0.1860
R_work r_work	0.1860
R_free r_free	0.2350

Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with a glutamyl-AMP analog

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

Glutamyl-tRNA synthetase 2

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

3afh__assembly_1__model_1

3afh__assembly_1__model_1 | I(q)

3afh__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) 7 domains

SCOP 2.08 (2 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Crystal structure of Thermotoga maritima nondiscriminating glutamyl-tRNA synthetase in complex with a glutamyl-AMP analog

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

Glutamyl-tRNA synthetase 2

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

3afh__assembly_1__model_1

3afh__assembly_1__model_1 | I(q)

3afh__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) 7 domains

SCOP 2.08 (2 domains)

CATH v4.4 (5 domains)

7. Citations (1)