SAXSdb — 3qpj

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Protease

Human immunodeficiency virus type 1 (BRU ISOLATE)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 3 4-({(3S,4S)-4-[(3-hydroxybenzyl)amino]pyrrolidin-3-yl}[4-(trifluoromethyl)benzyl]sulfamoyl)benzamide × 1 DITHIANE DIOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1BR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 501–599 Author chain B； PDBConstruct 1–99； UniProt 501–599

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_id	3qpj
Deposition date deposition_date	2011-02-14
Structure title title	HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor
Keywords keywords	Aspartyl Protease, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-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.

3qpj__assembly_1__model_1

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

Download this curve (.dat)

3qpj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3qpj__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	17.83 Å
Rg (electron density)	16.91 Å
Total Rg	17.87 Å
Atom count	1547
Residues	198
Excluded volume	28278 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3qpj__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 (5)

Entity 1 Entity 1 polymer

Description description	Protease
Molecular weight formula_weight	10804.8 kDa
EC 编号 ec_number	3.4.23.16
Mutation mutation	Q7K L33I L63I
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1824

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Source Source

Source organism organism	Human immunodeficiency virus type 1 (BRU ISOLATE)
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11686
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	4-({(3S,4S)-4-[(3-hydroxybenzyl)amino]pyrrolidin-3-yl}[4-(trifluoromethyl)benzyl]sulfamoyl)benzamide
Molecular weight formula_weight	548.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DITHIANE DIOL
Molecular weight formula_weight	152.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3qpja_
Class class	b — All beta proteins
Fold Fold fold	b.50 — Acid proteases
Superfamily Superfamily superfamily	b.50.1 — Acid proteases
Family Family family	b.50.1.1 — Retroviral protease (retropepsin)

Domain ID domain_id	d3qpjb_
Class class	b — All beta proteins
Fold Fold fold	b.50 — Acid proteases
Superfamily Superfamily superfamily	b.50.1 — Acid proteases
Family Family family	b.50.1.1 — Retroviral protease (retropepsin)

CATH v4.4 (2 domains)

Domain ID domain_id	3qpjA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

Domain ID domain_id	3qpjB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

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Unit-cell length a length_a	57.900 Å
Unit-cell length b length_b	85.980 Å
Unit-cell length c length_c	46.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.610 Å
Low-resolution limit resolution_low	20.151 Å
R factor r_factor	0.1711
R_work r_work	0.1677
R_free r_free	0.2025

HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protease

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3qpj__assembly_1__model_1

3qpj__assembly_1__model_1 | I(q)

3qpj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor

1. Protein Identity and Related Structures Protein Identity & Related Structures

Protease

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3qpj__assembly_1__model_1

3qpj__assembly_1__model_1 | I(q)

3qpj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)