SAXSdb — 3i8w

▼

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	COBALT BIS(1,2-DICARBOLLIDE) × 2 CHLORIDE ION × 2 GLYCEROL × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	COBALT BIS(1,2-DICARBOLLIDE) × 2 CHLORIDE ION × 2 GLYCEROL × 2 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

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3i8w
Deposition date deposition_date	2009-07-10
Structure title title	Crystal structure of a metallacarborane inhibitor bound to HIV protease
Keywords keywords	;inhibitor, cobalt bis(1, 2-dicarbollide), viral resistance, aspartic protease, AIDS, Aspartyl protease, Capsid maturation, Capsid protein, Cell membrane, DNA integration, DNA recombination, DNA-directed DNA polymerase, Endonuclease, Hydrolase, Lipoprotein, Magnesium, Membrane, Metal-binding, Multifunctional enzyme, Myristate, Nuclease, Nucleotidyltransferase, Nucleus, Phosphoprotein, Protease, RNA-binding, RNA-directed DNA polymerase, Transferase, Viral nucleoprotein, Virion, Zinc-finger, HYDROLASE-HYDROLASE INHIBITOR COMPLEX ;; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3i8w__assembly_1__model_1

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

Download this curve (.dat)

3i8w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3i8w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.21 Å
Rg (electron density)	17.98 Å
Total Rg	19.09 Å
Atom count	1564
Residues	198
Excluded volume	29117 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3i8w__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3i8w__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	947

PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Source Source

Source organism organism	Human immunodeficiency virus type 1
NCBI taxonomy ID ncbi_taxonomy_id	11686
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COBALT BIS(1,2-DICARBOLLIDE)
Molecular weight formula_weight	323.7 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	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	111

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3i8wa_
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 (1 domains)

Domain ID domain_id	3i8wA00
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

▶

Unit-cell length a length_a	58.158 Å
Unit-cell length b length_b	92.343 Å
Unit-cell length c length_c	48.952 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	C 2 2 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	23.780 Å
R factor r_factor	0.1778
R_work r_work	0.1760
R_free r_free	0.2119

Crystal structure of a metallacarborane inhibitor bound to HIV protease

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

3i8w__assembly_1__model_1

3i8w__assembly_1__model_1 | I(q)

3i8w__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of a metallacarborane inhibitor bound to HIV protease

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

3i8w__assembly_1__model_1

3i8w__assembly_1__model_1 | I(q)

3i8w__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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)