SAXSdb — 1az5

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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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 106–203	Mutation：S4H	No other associated polymer	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

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 1AZ5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YTI SIV PROTEASE CRYSTALLIZED WITH PEPTIDE PRODUCT Deposited 1996-08-01	Different mutation/modification Different oligomeric state Different experimental conditions 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 2.20 Å R-free 0.295
1YTJ SIV PROTEASE CRYSTALLIZED WITH PEPTIDE PRODUCT Deposited 1996-08-01	Different mutation/modification Different oligomeric state Different experimental conditions 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	1az5
Deposition date deposition_date	1997-11-25
Structure title title	UNLIGANDED SIV PROTEASE STRUCTURE IN AN "OPEN" CONFORMATION
Keywords keywords	HIV, AIDS, PROTEINASE, ASPARTYL PROTEASE, ENDONUCLEASE; ASPARTYL PROTEASE
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	14.72 Å
Radius of gyration Rg (electron density) rg_electron	13.48 Å
Forward intensity I(0) i0	2142350.00
Molecular weight molecular_weight	10335.0 kDa
Excluded volume excluded_volume	13130 Å³
Envelope volume envelope_volume	15692 Å³
Hydration-shell volume shell_volume	10305 Å³
Envelope diameter envelope_diameter	49.3 Å
Shell Rg shell_rg	18.69 Å
Envelope Rg envelope_rg	13.99 Å
Shape Rg shape_rg	13.53 Å
Total Rg total_rg	14.62 Å
Total atoms total_atoms	883
Residues n_residues	95
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	51.0 Å
Rg (real space) rg_real	14.69 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	2.1420e+06
I(0) uncertainty (real space) i0_real_error	2.4040e+04
Rg (reciprocal space) rg_reciprocal	14.69 Å
I(0) (reciprocal space) i0_reciprocal	2142000.0000
Solution quality estimate total_estimate	0.7664
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.4 Å
Skewness Skewness skewness	0.341
Kurtosis Kurtosis kurtosis	-0.036
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	564700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.655; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1az5a_
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	1az5A00
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 (2)

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Unit-cell length a length_a	45.400 Å
Unit-cell length b length_b	45.400 Å
Unit-cell length c length_c	87.900 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.2040
R_work r_work	0.2040
R_free r_free	0.2660

Description description	SIV PROTEASE
Molecular weight formula_weight	10768.4 kDa
EC 编号 ec_number	3.4.23.16
Mutation mutation	S4H
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	940

UNLIGANDED SIV PROTEASE STRUCTURE IN AN "OPEN" CONFORMATION

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

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

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

fit	/app/data/saxs_computation/az/1az5/1az5.fit
pddf	/app/data/pr_computation/az/1az5/1az5.pr.out
profile	/app/data/saxs_computation/az/1az5/1az5.dat