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1kog

Crystal structure of E. coli threonyl-tRNA synthetase interacting with the essential domain of its mRNA operator

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Threonyl-tRNA synthetase

Escherichia coli

UniProt P0A8M3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Homooligomer Protein 2 RNA 2 Threonyl-tRNA synthetase mRNA × 2 ZINC ION × 2 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE × 2 water × 4 Consistent with all polymers
2 Protein–RNA Homooligomer Protein 2 RNA 2 Threonyl-tRNA synthetase mRNA × 2 ZINC ION × 2 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE × 2 water × 4 Consistent with all polymers
3 Protein–RNA Homooligomer Protein 2 RNA 2 Threonyl-tRNA synthetase mRNA × 2 ZINC ION × 2 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE × 2 water × 4 Consistent with all polymers
4 Protein–RNA Homooligomer Protein 2 RNA 2 Threonyl-tRNA synthetase mRNA × 2 ZINC ION × 2 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE × 2 water × 4 Consistent with all polymers
5 Protein–RNA Homooligomer Protein 2 RNA 2 Threonyl-tRNA synthetase mRNA × 2 ZINC ION × 2 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE × 2 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1tje 1tke 1tkg 1tky

4 assemblies

Homodimer
1evk 1evl 1evl 1fyf 4hwo 4hwp 4hwr 4hws 4p3o 4p3p 8h98

11 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1kog 1kog 1kog 1kog 1kog 1qf6

6 assemblies

View Construct and Data Evidence
UniProt name SYT_ECOLI
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–401； UniProt 242–642 Author chain B； PDBConstruct 1–401； UniProt 242–642 Author chain C； PDBConstruct 1–401； UniProt 242–642 Author chain D； PDBConstruct 1–401； UniProt 242–642 Author chain E； PDBConstruct 1–401； UniProt 242–642 Author chain F； PDBConstruct 1–401； UniProt 242–642 Author chain G； PDBConstruct 1–401； UniProt 242–642 Author chain H； PDBConstruct 1–401； UniProt 242–642

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_id1kog
Deposition date deposition_date2001-12-20
Structure title titleCrystal structure of E. coli threonyl-tRNA synthetase interacting with the essential domain of its mRNA operator
Keywords keywordsProtein-RNA complex, RNA stem-loop, RNA double helix, RNA base triples, LIGASE-RNA COMPLEX; LIGASE/RNA
Experimental Method methodX-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.

1kog__assembly_1__model_1

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

Download this curve (.dat)

1kog__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1kog__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）32.95 Å
Rg (electron density)30.73 Å
Total Rg31.56 Å
Atom count8188
Residues876
Excluded volume139380 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1kog__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1kog__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1kog__assembly_3__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1kog__assembly_4__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 1kog__assembly_5__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 (5)

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_idd1koga1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1koga2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
Domain ID domain_idd1kogb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1kogb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
Domain ID domain_idd1kogc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1kogc2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
Domain ID domain_idd1kogd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1kogd2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
Domain ID domain_idd1koge1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1koge2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
Domain ID domain_idd1kogf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1kogf2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
Domain ID domain_idd1kogg1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1kogg2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
Domain ID domain_idd1kogh1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.51 — Anticodon-binding domain-like
Superfamily Superfamily superfamilyc.51.1 — Class II aaRS ABD-related
Family Family familyc.51.1.1 — Anticodon-binding domain of Class II aaRS
Domain ID domain_idd1kogh2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamilyd.104.1 — Class II aaRS and biotin synthetases
Family Family familyd.104.1.1 — Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain

CATH v4.4 (16 domains)

Domain ID domain_id1kogA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1kogA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id1kogB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1kogB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id1kogC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1kogC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id1kogD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1kogD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id1kogE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1kogE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id1kogF01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1kogF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id1kogG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1kogG02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id1kogH01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id1kogH02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
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7. Citations (1)