SAXSdb — 1yti

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

SIV PROTEASE

Simian immunodeficiency virus

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 106–203	Mutation：CHAIN A, S4H	PEPTIDE PRODUCT × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 Å R-free 0.295

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 1YTI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AZ5 UNLIGANDED SIV PROTEASE STRUCTURE IN AN "OPEN" CONFORMATION Deposited 1997-11-25	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 106–203（98 aa）	Mutation：S4H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；100 MM SODIUM CACODYLATE, PH 6.5, 0.3 M NACL	Resolution 2.00 Å R-free 0.266
1YTJ SIV PROTEASE CRYSTALLIZED WITH PEPTIDE PRODUCT Deposited 1996-08-01	Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 106–203（98 aa）	Mutation：CHAIN A, S4H	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.285

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POL_SIVM1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–98； UniProt 106–203

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	1yti
Deposition date deposition_date	1996-08-01
Structure title title	SIV PROTEASE CRYSTALLIZED WITH PEPTIDE PRODUCT
Keywords keywords	;COMPLEX (HYDROLASE-PEPTIDE, ) AIDS, POLYPROTEIN, HYDROLASE, ASPARTYL PROTEASE, ENDONUCLEASE, RNA-DIRECTED DNA POLYMERASE, COMPLEX (HYDROLASE-PEPTIDE) COMPLEX ;; COMPLEX (HYDROLASE/PEPTIDE)
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	14.98 Å
Radius of gyration Rg (electron density) rg_electron	13.68 Å
Forward intensity I(0) i0	2382810.00
Molecular weight molecular_weight	11028.0 kDa
Excluded volume excluded_volume	14056 Å³
Envelope volume envelope_volume	16902 Å³
Hydration-shell volume shell_volume	10844 Å³
Envelope diameter envelope_diameter	49.9 Å
Shell Rg shell_rg	19.00 Å
Envelope Rg envelope_rg	14.10 Å
Shape Rg shape_rg	13.75 Å
Total Rg total_rg	14.83 Å
Total atoms total_atoms	779
Residues n_residues	103
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

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

Maximum dimension Dmax dmax	53.3 Å
Rg (real space) rg_real	14.93 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	2.3830e+06
I(0) uncertainty (real space) i0_real_error	3.0780e+04
Rg (reciprocal space) rg_reciprocal	14.93 Å
I(0) (reciprocal space) i0_reciprocal	2383000.0000
Solution quality estimate total_estimate	0.8362
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.267
Kurtosis Kurtosis kurtosis	-0.148
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	614000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.628; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.999

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SIV PROTEASE
Molecular weight formula_weight	10768.4 kDa
EC 编号 ec_number	3.4.23.16
Mutation mutation	CHAIN A, S4H
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	798

PQFHLWKRPVVTAHIEGQPVEVLLDTGADDSIVTGIELGPHYTPKIVGGIGGFINTKEYKNVEVEVLGKRIKGTIMTGDTPINIFGRNLLTALGMSLNF

来源 Source

来源生物 organism	Simian immunodeficiency virus
NCBI Class编号 ncbi_taxonomy_id	11723
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PEPTIDE PRODUCT
Molecular weight formula_weight	536.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

FLEK

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ytia_
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	1ytiA00
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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8. Citations (1)

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Unit-cell length a length_a	63.700 Å
Unit-cell length b length_b	32.500 Å
Unit-cell length c length_c	97.700 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 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2950

fit	/app/data/saxs_computation/yt/1yti/1yti.fit
pddf	/app/data/pr_computation/yt/1yti/1yti.pr.out
profile	/app/data/saxs_computation/yt/1yti/1yti.dat

SIV PROTEASE CRYSTALLIZED WITH PEPTIDE PRODUCT

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

SIV 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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)