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5xpa

Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 9'U10' on the target strand

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

Uncharacterized protein Ago

Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)

UniProt Q746M7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Monomer Protein 1 DNA 1 RNA 1 ;DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3') ; × 1 ;RNA (5'-R(P*AP*UP*AP*CP*AP*AP*CP*CP*GP*UP*UP*CP*UP*AP*CP*UP*CP*CP*G)-3') ; × 1 MAGNESIUM ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3dlb 3dlh 3dlh 3f73 3f73 3hjf 3hk2 3hk2 3hm9 3ho1 3hvr 3hvr

31 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name Q746M7_THET2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–685； UniProt 1–685

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_id5xpa
Deposition date deposition_date2017-06-01
Structure title titleCrystal structure of T. thermophilus Argonaute protein complexed with a bulge 9'U10' on the target strand
Keywords keywordsArgonaute, miRNA, bulge, mismatch, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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.

5xpa__assembly_1__model_1

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

Download this curve (.dat)

5xpa__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.

5xpa__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）28.96 Å
Rg (electron density)28.74 Å
Total Rg29.34 Å
Atom count5967
Residues719
Excluded volume103500 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5xpa__assembly_1__model_1 trimeric （3） 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 (4)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id5xpaA01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology260 — paz domain
Homologous superfamily homologous superfamily50 —
Domain ID domain_id5xpaA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily2300 — Response regulator
Domain ID domain_id5xpaA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
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7. Citations (1)