SAXSdb — 9zye

▼

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

HTLV-1 Protease

Human T-cell leukemia virus type I

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 27–142 Chain B； UniProt 27–142	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 A60 (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-1-benzyl-2-hydroxypropyl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2	Resolution 2.70 Å R-free 0.282

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ZYE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6W6Q WT HTLV-1 Protease in Complex with Darunavir (DRV) Deposited 2020-03-17	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–142（116 aa） Chain B 27–142（116 aa）	Not recorded	017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2	Resolution 2.10 Å R-free 0.264
6W6R WT HTLV-1 Protease in Complex with UMass6 (UM6) Deposited 2020-03-17	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–142（116 aa） Chain B 27–142（116 aa）	Not recorded	A60 (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-1-benzyl-2-hydroxypropyl]carbamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2	Resolution 2.05 Å R-free 0.242
6W6S WT HTLV-1 Protease in Complex with Phosphonated UMass6 (PU6) Deposited 2020-03-17	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–142（116 aa） Chain B 27–142（116 aa）	Not recorded	TK7 diethyl [(4-{(2S,3R)-4-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-2-[({[(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl]oxy}carbonyl)amino]-3-hydroxybutyl}phenoxy)methyl]phosphonate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2	Resolution 2.29 Å R-free 0.306
9ZVR Crystal structure of HTLV-1 protease bound to darunavir at 2.1 angstroms with truncated flaps Deposited 2025-12-30	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 27–142（116 aa） Chain B 27–142（116 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 017 (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE × 1 DMS DIMETHYL SULFOXIDE × 1 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；293 K；39-41% (v/v) PEG 300, 0.1M Phosphate/Citrate Buffer pH 4.2	Resolution 2.10 Å R-free 0.253

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A1Y1C9N2_9DELA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 27–142 Author chain B； PDBConstruct 1–116； UniProt 27–142

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	9zye
Deposition date deposition_date	2026-01-05
最后修订 last_revision	2026-01-21
Structure title title	Crystal structure of HTLV-1 protease bound to UMass6 at 2.7 angstroms with truncated flaps
Keywords keywords	;HTLV-1, PROTEASE, DRUG RESISTANCE, PROTEASE INHIBITOR, COMPLEX, HYDROLASE INHIBITOR COMPLEX, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, VIRAL PROTEIN, VIRAL PROTEIN-INHIBITOR complex ;; VIRAL PROTEIN/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.33 Å
Radius of gyration Rg (electron density) rg_electron	18.36 Å
Forward intensity I(0) i0	8174780.00
Molecular weight molecular_weight	22818.0 kDa
Excluded volume excluded_volume	29365 Å³
Envelope volume envelope_volume	33574 Å³
Hydration-shell volume shell_volume	15958 Å³
Envelope diameter envelope_diameter	63.9 Å
Shell Rg shell_rg	23.79 Å
Envelope Rg envelope_rg	18.61 Å
Shape Rg shape_rg	18.37 Å
Total Rg total_rg	19.26 Å
Total atoms total_atoms	1665
Residues n_residues	209
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.0 Å
Rg (real space) rg_real	19.37 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	8.1750e+06
I(0) uncertainty (real space) i0_real_error	1.0890e+05
Rg (reciprocal space) rg_reciprocal	19.36 Å
I(0) (reciprocal space) i0_reciprocal	8175000.0000
Solution quality estimate total_estimate	0.7878
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.410
Kurtosis Kurtosis kurtosis	-0.315
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2345000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.769; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	HTLV-1 Protease
Molecular weight formula_weight	12566.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	1804

PVIPLDPARRPVIKAQVDTQTSHPKTIEALLDTGADMTVIPIALFSSNTPLKNTSVLGAGGQTQDHFKLTSLPVLIRLPFRTTPIVLTSCLVDTKNNWAIIGRDALQQCQGVLYLP

来源 Source

来源生物 organism	Human T-cell leukemia virus type I
NCBI Class编号 ncbi_taxonomy_id	11908
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	;(3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl [(1S,2R)-3-{[(4-aminophenyl)sulfonyl](2-ethylbutyl)amino}-1-benzyl-2-hydroxypropyl]carbamate ;
Molecular weight formula_weight	575.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	92

▶

8. Citations (1)

▶

Unit-cell length a length_a	77.753 Å
Unit-cell length b length_b	77.753 Å
Unit-cell length c length_c	159.132 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	hexagonal

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	41.670 Å
R factor r_factor	0.2254
R_work r_work	0.2225
R_free r_free	0.2820

fit	/app/data/saxs_computation/zy/9zye/9zye.fit
pddf	/app/data/pr_computation/zy/9zye/9zye.pr.out
profile	/app/data/saxs_computation/zy/9zye/9zye.dat

Crystal structure of HTLV-1 protease bound to UMass6 at 2.7 angstroms with truncated flaps

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

HTLV-1 Protease

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction