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1k6y

Crystal Structure of a Two-Domain Fragment of HIV-1 Integrase

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

Integrase

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 4 ZINC ION × 4 POTASSIUM ION × 4 PHOSPHATE ION × 4 water × 4 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 4 ZINC ION × 4 POTASSIUM ION × 4 PHOSPHATE ION × 4 water × 4 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 2 ZINC ION × 2 POTASSIUM ION × 2 PHOSPHATE ION × 2 water × 2 Consistent with protein count
4 Protein homooligomer Homooligomer Protein 2 ZINC ION × 2 POTASSIUM ION × 2 PHOSPHATE ION × 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 1–212； UniProt 716–927 Author chain B； PDBConstruct 1–212； UniProt 716–927 Author chain C； PDBConstruct 1–212； UniProt 716–927 Author chain D； PDBConstruct 1–212； UniProt 716–927

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_id1k6y
Deposition date deposition_date2001-10-17
Structure title titleCrystal Structure of a Two-Domain Fragment of HIV-1 Integrase
Keywords keywordsHIV-1, integrase, domain organization, TRANSFERASE; TRANSFERASE
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.

1k6y__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1k6y__assembly_3__model_1 | I(q)

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

1k6y__assembly_3__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）23.59 Å
Rg (electron density)22.25 Å
Total Rg23.28 Å
Atom count2998
Residues386
Excluded volume53501 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1k6y__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 1k6y__assembly_2__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 1k6y__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 1k6y__assembly_4__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 (5)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1k6ya1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.10 — Retroviral integrase, N-terminal Zn binding domain
Family Family familya.4.10.1 — HIV/SIV integrase, N-terminal Zn binding domain
Domain ID domain_idd1k6ya2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.2 — Retroviral integrase, catalytic domain
Domain ID domain_idd1k6yb1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.10 — Retroviral integrase, N-terminal Zn binding domain
Family Family familya.4.10.1 — HIV/SIV integrase, N-terminal Zn binding domain
Domain ID domain_idd1k6yb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.2 — Retroviral integrase, catalytic domain
Domain ID domain_idd1k6yc1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.10 — Retroviral integrase, N-terminal Zn binding domain
Family Family familya.4.10.1 — HIV/SIV integrase, N-terminal Zn binding domain
Domain ID domain_idd1k6yc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.2 — Retroviral integrase, catalytic domain
Domain ID domain_idd1k6yd1
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.10 — Retroviral integrase, N-terminal Zn binding domain
Family Family familya.4.10.1 — HIV/SIV integrase, N-terminal Zn binding domain
Domain ID domain_idd1k6yd2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.2 — Retroviral integrase, catalytic domain

CATH v4.4 (8 domains)

Domain ID domain_id1k6yA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily200 — Integrase, N-terminal zinc-binding domain
Domain ID domain_id1k6yA02
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_id1k6yB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily200 — Integrase, N-terminal zinc-binding domain
Domain ID domain_id1k6yB02
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_id1k6yC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily200 — Integrase, N-terminal zinc-binding domain
Domain ID domain_id1k6yC02
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_id1k6yD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily200 — Integrase, N-terminal zinc-binding domain
Domain ID domain_id1k6yD02
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)