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4nyf

HIV integrase in complex with inhibitor

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

Integrase

Human immunodeficiency virus type 1

UniProt P0C6F2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 (2S)-tert-butoxy[4-(4-chlorophenyl)-2-methylquinolin-3-yl]ethanoic acid × 1 CADMIUM ION × 4 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3lp3 3lp3

2 assemblies

Homodimer
3lp3 3th9 3vfa 4i8w 4i8z 4mc1 4mc2 4mc6 4mc9 4nyf 4qgi

11 assemblies

Homotetramer

None

Other homooligomers
9ja0

1 assemblies

Heteromeric or nucleic-acid complex
5k14 6y9v 6y9w 6y9x 6y9y 6y9z

6 assemblies

View Construct and Data Evidence
UniProt name POL_HV1LW
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 10–168； UniProt 1199–1357 Author chain B； PDBConstruct 10–168； UniProt 1199–1357

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_id4nyf
Deposition date deposition_date2013-12-10
Structure title titleHIV integrase in complex with inhibitor
Keywords keywordsAllosteric Inhibitor, NCINI, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/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.

4nyf__assembly_1__model_1

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

Download this curve (.dat)

4nyf__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.

4nyf__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）19.29 Å
Rg (electron density)17.89 Å
Total Rg18.97 Å
Atom count2251
Residues289
Excluded volume40320 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4nyf__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 (4)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4nyfa_
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_idd4nyfb_
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 (2 domains)

Domain ID domain_id4nyfA00
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_id4nyfB00
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)