SAXSdb — 4ep3

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

protease, tethered dimer

HIV-1 M:B_ARV2/SF2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	substrate CA-p2 × 1 （Q9YP46） GLYCEROL × 3 BETA-MERCAPTOETHANOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1A2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 491–589 Author chain A； PDBConstruct 105–203； UniProt 491–589

substrate CA-p2

OrganismNot specified

UniProt Q9YP46

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	protease, tethered dimer × 1 （P03369） GLYCEROL × 3 BETA-MERCAPTOETHANOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9YP46_9HIV1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–9； UniProt 359–367

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	4ep3
Deposition date deposition_date	2012-04-16
Structure title title	Crystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate CA-p2
Keywords keywords	;HIV-1 protease, specificity design, drug design, Protease inhibitors, AIDS, Aspartyl protease, HYDROLASE, hydrolase-hydrolase substrate complex ;; hydrolase/hydrolase substrate
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.

4ep3__assembly_1__model_1

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

Download this curve (.dat)

4ep3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ep3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.96 Å
Rg (electron density)	16.99 Å
Total Rg	17.89 Å
Atom count	1564
Residues	207
Excluded volume	28510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ep3__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, tethered dimer
Molecular weight formula_weight	22005.0 kDa
EC 编号 ec_number	3.4.23.16
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1660

PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEILGHKAIGTVLVGPTPVNIIGRNLLTQIGMTLNFGGSSGPQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEILGHKAIGTVLVGPTPVNIIGRNLLTQIGMTLNF

Source Source

Source organism organism	HIV-1 M:B_ARV2/SF2
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11685
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	substrate CA-p2
Molecular weight formula_weight	990.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

KARVLAEAM

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 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	62

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4ep3A01
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	4ep3A02
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	51.046 Å
Unit-cell length b length_b	58.935 Å
Unit-cell length c length_c	61.451 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	42.530 Å
R factor r_factor	0.1905
R_work r_work	0.1886
R_free r_free	0.2269

Crystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate CA-p2

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

protease, tethered dimer

State in the Current Structure

Other States of the Same Protein in the Database

substrate CA-p2

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

4ep3__assembly_1__model_1

4ep3__assembly_1__model_1 | I(q)

4ep3__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of inactive single chain wild-type HIV-1 Protease in Complex with the substrate CA-p2

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

protease, tethered dimer

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

substrate CA-p2

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

4ep3__assembly_1__model_1

4ep3__assembly_1__model_1 | I(q)

4ep3__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)