SAXSdb — 1bh6

▼

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

SUBTILISIN DY

OrganismNot specified

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–274	Not recorded	CA CALCIUM ION × 1 NA SODIUM ION × 1 1BH N-BENZYLOXYCARBONYL-ALA-PRO-3-AMINO-4-PHENYL-BUTAN-2-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；AS GIVEN IN REFERENCE 1, pH 6.0	Resolution 1.75 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	SUBD_BACLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–274； UniProt 1–274

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	1bh6
Deposition date deposition_date	1998-06-15
Structure title title	SUBTILISIN DY IN COMPLEX WITH THE SYNTHETIC INHIBITOR N-BENZYLOXYCARBONYL-ALA-PRO-PHE-CHLOROMETHYL KETONE
Keywords keywords	HYDROLASE, SUBTILISIN, PROTEIN DEGRADATION; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	17.83 Å
Radius of gyration Rg (electron density) rg_electron	16.52 Å
Forward intensity I(0) i0	14147800.00
Molecular weight molecular_weight	28011.0 kDa
Excluded volume excluded_volume	34919 Å³
Envelope volume envelope_volume	37163 Å³
Hydration-shell volume shell_volume	18262 Å³
Envelope diameter envelope_diameter	54.2 Å
Shell Rg shell_rg	23.31 Å
Envelope Rg envelope_rg	16.76 Å
Shape Rg shape_rg	16.52 Å
Total Rg total_rg	17.51 Å
Total atoms total_atoms	1971
Residues n_residues	274
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	55.6 Å
Rg (real space) rg_real	17.66 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	1.4150e+07
I(0) uncertainty (real space) i0_real_error	1.4790e+05
Rg (reciprocal space) rg_reciprocal	17.68 Å
I(0) (reciprocal space) i0_reciprocal	14150000.0000
Solution quality estimate total_estimate	0.8072
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.017
Kurtosis Kurtosis kurtosis	-0.541
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4900000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SUBTILISIN DY
Molecular weight formula_weight	27499.4 kDa
EC 编号 ec_number	3.4.21.62
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2210

AQTVPYGIPLIKADKVQAQGYKGANVKVGIIDTGIASSHTDLKVVGGASFVSGESYNTDGNGHGTHVAGTVAALDNTTGVLGVAPNVSLYAIKVLNSSGSGSYSAIVSGIEWATQNGLDVINMSLGGPSGSTALKQAVDKAYASGIVVVAAAGNSGNSGSQNTIGYPAKYDSVIAVGAVDSNKNRASFSSVGSELEVMAPGVSVYSTYPSNTYTSLNGTSMASPHVAGAAALILSKYPTLSASQVRNRLSSTATNLGDSFYYGKGLINVEAAAQ

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	N-BENZYLOXYCARBONYL-ALA-PRO-3-AMINO-4-PHENYL-BUTAN-2-OL
Molecular weight formula_weight	467.6 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	226

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bh6a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.41 — Subtilisin-like
Superfamily Superfamily superfamily	c.41.1 — Subtilisin-like
Family Family family	c.41.1.1 — Subtilases

CATH v4.4 (1 domains)

Domain ID domain_id	1bh6A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	200 — Peptidase S8/S53 domain

▶

8. Citations (2)

▶

Unit-cell length a length_a	52.830 Å
Unit-cell length b length_b	72.750 Å
Unit-cell length c length_c	59.890 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1400
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/bh/1bh6/1bh6.fit
pddf	/app/data/pr_computation/bh/1bh6/1bh6.pr.out
profile	/app/data/saxs_computation/bh/1bh6/1bh6.dat

SUBTILISIN DY IN COMPLEX WITH THE SYNTHETIC INHIBITOR N-BENZYLOXYCARBONYL-ALA-PRO-PHE-CHLOROMETHYL KETONE

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

SUBTILISIN DY

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