SAXSdb — 1bqy

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：PLASMINOGEN ACTIVATOR × 2 缺少 UniProt 身份时不显示参考序列区间	Not recorded	0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 Å R-free 0.258
2	Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric	Entity 1：PLASMINOGEN ACTIVATOR × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 Å R-free 0.258
3	Protein monomer Monomer 蛋白 1 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: monomeric	Entity 1：PLASMINOGEN ACTIVATOR × 1 缺少 UniProt 身份时不显示参考序列区间	Not recorded	0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 Å R-free 0.258

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	1bqy
Deposition date deposition_date	1998-08-20
Structure title title	Plasminogen activator (TSV-PA) from snake venom
Keywords keywords	FIBRINOLYSIS, PLASMINOGEN ACTIVATOR, SERINE PROTEINASE, SNAKE VENOM, HYDROLASE-HYDROLASE INHIBITOR COMPLEX, BLOOD CLOTTING; HYDROLASE/HYDROLASE INHIBITOR
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	48.04 Å
Radius of gyration Rg (electron density) rg_electron	48.69 Å
Forward intensity I(0) i0	79155900.00
Molecular weight molecular_weight	48355.0 kDa
Excluded volume excluded_volume	46334 Å³
Envelope volume envelope_volume	98429 Å³
Hydration-shell volume shell_volume	16680 Å³
Envelope diameter envelope_diameter	143.2 Å
Shell Rg shell_rg	55.67 Å
Envelope Rg envelope_rg	45.38 Å
Shape Rg shape_rg	48.69 Å
Total Rg total_rg	48.87 Å
Total atoms total_atoms	3644
Residues n_residues	468
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	142.5 Å
Rg (real space) rg_real	48.90 Å
Rg uncertainty (real space) rg_real_error	1.69 Å
I(0) (real space) i0_real	7.9160e+07
I(0) uncertainty (real space) i0_real_error	1.4650e+06
Rg (reciprocal space) rg_reciprocal	48.05 Å
I(0) (reciprocal space) i0_reciprocal	79070000.0000
Solution quality estimate total_estimate	0.5405
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.156
Kurtosis Kurtosis kurtosis	-1.595
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	917200.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.000; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.022

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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	PLASMINOGEN ACTIVATOR
Molecular weight formula_weight	25634.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3806

VFGGDECNINEHRSLVVLFNSNGFLCGGTLINQDWVVTAAHCDSNNFQLLFGVHSKKILNEDEQTRDPKEKFFCPNRKKDDEVDKDIMLIKLDSSVSNSEHIAPLSLPSSPPSVGSVCRIMGWGKTIPTKEIYPDVPHCANINILDHAVCRTAYSWRQVANTTLCAGILQGGRDTCHFDSGGPLICNGIFQGIVSWGGHPCGQPGEPGVYTKVFDYLDWIKSIIAGNKDATCPP

来源 Source

来源生物 organism	Viridovipera stejnegeri
通用名 common_name	;Stejneger's pit viper ;
NCBI Class编号 ncbi_taxonomy_id	39682
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide
Molecular weight formula_weight	395.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	162

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bqya_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d1bqyb_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (4 domains)

Domain ID domain_id	1bqyA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1bqyA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1bqyB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1bqyB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (1)

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Unit-cell length a length_a	45.290 Å
Unit-cell length b length_b	67.420 Å
Unit-cell length c length_c	163.670 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1780
R_work r_work	0.1780
R_free r_free	0.2580

fit	/app/data/saxs_computation/bq/1bqy/1bqy.fit
pddf	/app/data/pr_computation/bq/1bqy/1bqy.pr.out
profile	/app/data/saxs_computation/bq/1bqy/1bqy.dat

Plasminogen activator (TSV-PA) from snake venom

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

Assembly Composition of the Current Entry

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