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3dox

X-ray structure of HIV-1 protease in situ product complex

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

HIV-1 PROTEASE

Human immunodeficiency virus type 1 (isolate HXB2 group M subtype B)

UniProt P04585

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 A PEPTIDE SUBSTRATE-SQNY × 1 A PEPTIDE SUBSTRATE-PIV × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1esk 1g6l 1lv1 1o1w 1tam 3kt2 3kt5 3n3i 4kse 4q5m

10 assemblies

Homodimer
1bv7 1bv9 1bve 1bvg 1bwa 1bwb 1c0t 1c0u 1c1b 1c1c 1dmp 1dtq

130 assemblies; showing the first 12

Homotetramer
1ex4 1ex4 1ex4 1ex4 3di6 3ffi 3i0r 3i0s 3lp0 3lp1 3lp2 3qip

17 assemblies; showing the first 12

Other homooligomers
1ex4 1ex4 1ex4 1ex4 1ex4

5 assemblies

Heteromeric or nucleic-acid complex
1a30 1ncp 1rtd 1rtd 1t05 2hnz 3dox 3kjv 3kk1 3kk2 3kk3 3qin

40 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name POL_HV1H2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–99； UniProt 489–587 Author chain A； PDBConstruct 105–203； UniProt 489–587

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_id3dox
Deposition date deposition_date2008-07-07
Structure title titleX-ray structure of HIV-1 protease in situ product complex
Keywords keywords;HIV-1 protease; transition state; reaction intermediate; catalysis; inhibitor; X-ray Crystallography, AIDS, Aspartyl protease, Capsid maturation, Capsid protein, Cytoplasm, DNA integration, DNA recombination, DNA-directed DNA polymerase, Endonuclease, Host-virus interaction, Hydrolase, Lipoprotein, Magnesium, Metal-binding, Multifunctional enzyme, Myristate, Nuclease, Nucleotidyltransferase, Nucleus, Phosphoprotein, Protease, Ribosomal frameshifting, RNA-binding, RNA-directed DNA polymerase, Transferase, Viral nucleoprotein, Virion, Zinc, Zinc-finger ;; HYDROLASE
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.

3dox__assembly_1__model_1

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

Download this curve (.dat)

3dox__assembly_1__model_1 | I(q)

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

3dox__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）18.00 Å
Rg (electron density)17.08 Å
Total Rg18.12 Å
Atom count1573
Residues205
Excluded volume28686 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3dox__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) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3doxA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
Domain ID domain_id3doxA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily10 — Acid Proteases
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7. Citations (5)