SAXSdb — 3dk1

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

Protease

Human immunodeficiency virus type 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SODIUM ION × 1 CHLORIDE ION × 3 ;(4aR,6r,7aS)-hexahydro-4aH-cyclopenta[b][1,4]dioxin-6-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate ; × 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	3dk1
Deposition date deposition_date	2008-06-24
Structure title title	Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0105A
Keywords keywords	;HIV-1, wild type protease, protease inhibitor, HYDROLASE, AIDS, Aspartyl protease, Capsid maturation, Capsid protein, Cytoplasm, DNA integration, DNA recombination, DNA-directed DNA polymerase, Endonuclease, 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 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.

3dk1__assembly_1__model_1

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

Download this curve (.dat)

3dk1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dk1__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.12 Å
Rg (electron density)	17.13 Å
Total Rg	18.20 Å
Atom count	1556
Residues	198
Excluded volume	28556 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dk1__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	10740.7 kDa
EC 编号 ec_number	3.4.23.16
Mutation mutation	Q7K, L33I, L63I, C67A, C95A, Q107K, L133I, L163I, C167A, C195A
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	1955

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Source Source

Source organism organism	Human immunodeficiency virus type 1
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	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	;(4aR,6r,7aS)-hexahydro-4aH-cyclopenta[b][1,4]dioxin-6-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate ;
Molecular weight formula_weight	576.7 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	201

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3dk1a_
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	d3dk1b_
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	3dk1A00
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	3dk1B00
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	58.003 Å
Unit-cell length b length_b	86.338 Å
Unit-cell length c length_c	45.833 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	1.070 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1519
R_work r_work	0.1505
R_free r_free	0.1769

Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0105A

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

3dk1__assembly_1__model_1

3dk1__assembly_1__model_1 | I(q)

3dk1__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)

Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0105A

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

3dk1__assembly_1__model_1

3dk1__assembly_1__model_1 | I(q)

3dk1__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)