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3ao4

Fragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase

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

POL polyprotein

Human immunodeficiency virus 1

UniProt Q72498

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 CADMIUM ION × 4 CHLORIDE ION × 2 SULFATE ION × 3 3-(1,3-benzodioxol-5-yl)-1-methyl-1H-pyrazol-5-amine × 2 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1k6y 1k6y 3ao1 3ao2 3ao3 3ao4 3l3u 3vq4 3vq5 3vq6 3vq8 3vq9

20 assemblies; showing the first 12

Homotetramer
1k6y 1k6y 8cta 8cta 8cta 8cta

6 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
3ao5 3l3v 3ovn 3vq7 3vqa 3vqq

6 assemblies

View Construct and Data Evidence
UniProt name Q72498_9HIV1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–163； UniProt 765–927 Author chain B； PDBConstruct 1–163； UniProt 765–927

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_id3ao4
Deposition date deposition_date2010-09-20
Structure title titleFragment-based approach to the design of ligands targeting a novel site on HIV-1 integrase
Keywords keywords;DNA INTEGRATION, AIDS, INTEGRASE, ENDONUCLEASE, POLYNUCLEOTIDYL TRANSFERASE, DNA BINDING, VIRAL PROTEIN, RNaseH, fragment binding, VIRAL PROTEIN-TRANSFERASE INHIBITOR complex ;; VIRAL PROTEIN/TRANSFERASE INHIBITOR
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.

3ao4__assembly_1__model_1

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

Download this curve (.dat)

3ao4__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3ao4__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）18.83 Å
Rg (electron density)17.45 Å
Total Rg18.56 Å
Atom count2148
Residues272
Excluded volume38214 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3ao4__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 (6)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3ao4A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id3ao4B00
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)