SAXSdb — 1by7

▼

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

PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-2)

Homo sapiens

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 1–415	Mutation：RESIDUES 66 - 98 EXCISED	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.268

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 1BY7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JRR HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETIONMUTANT] COMPLEXED WITH PEPTIDE MIMIckING THE REACTIVE CENTER LOOP Deposited 2001-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–415（415 aa） Chain P 367–380（14 aa） Fragment：RESIDUES 367-380	Mutation：RESIDUES 66 - 98 EXCISED Non-standard monomer：Yes (specific site not provided by mmCIF)	BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；PEG 8000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.60 Å R-free 0.225
2ARQ Human plasminogen activator inhibitor-2.[loop (66-98) deletion mutant] complexed with peptide n-acetyl-teaaagdggvmtgr-oh Deposited 2005-08-21	Different construct 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 1–415（415 aa） Chain P 366–380（15 aa）	Mutation：T373D Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 8K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.85 Å R-free 0.248
2ARR Human plasminogen activator inhibitor-2.[loop (66-98) deletion mutant] complexed with peptide n-acetyl-teaaagmggvmtgr-oh Deposited 2005-08-21	Different construct 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 1–415（415 aa） Chain P 366–380（15 aa）	Mutation：T8M Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；peg 8K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.55 Å R-free 0.220

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PAI2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–382； UniProt 1–415

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	1by7
Deposition date deposition_date	1998-10-27
Structure title title	HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2. LOOP (66-98) DELETION MUTANT
Keywords keywords	SERPIN, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	22.46 Å
Radius of gyration Rg (electron density) rg_electron	21.15 Å
Forward intensity I(0) i0	26661100.00
Molecular weight molecular_weight	40325.0 kDa
Excluded volume excluded_volume	50780 Å³
Envelope volume envelope_volume	58496 Å³
Hydration-shell volume shell_volume	23127 Å³
Envelope diameter envelope_diameter	72.4 Å
Shell Rg shell_rg	27.78 Å
Envelope Rg envelope_rg	21.37 Å
Shape Rg shape_rg	21.14 Å
Total Rg total_rg	22.05 Å
Total atoms total_atoms	2836
Residues n_residues	354
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	72.4 Å
Rg (real space) rg_real	22.42 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	2.6660e+07
I(0) uncertainty (real space) i0_real_error	3.4130e+05
Rg (reciprocal space) rg_reciprocal	22.43 Å
I(0) (reciprocal space) i0_reciprocal	26660000.0000
Solution quality estimate total_estimate	0.7324
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.324
Kurtosis Kurtosis kurtosis	-0.375
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6728000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 0.328; Positv: 1.000; Valcen: 1.000; Smooth: 0.949

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1by7a_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.1 — Serpins
Superfamily Superfamily superfamily	e.1.1 — Serpins
Family Family family	e.1.1.1 — Serpins

CATH v4.4 (2 domains)

Domain ID domain_id	1by7A01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily	10 — Alpha-1-antitrypsin, domain 1

Domain ID domain_id	1by7A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily	10 — Antithrombin, subunit I, domain 2

▶

8. Citations (1)

▶

Unit-cell length a length_a	138.820 Å
Unit-cell length b length_b	41.730 Å
Unit-cell length c length_c	77.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2020
R_free r_free	0.2680

Description description	PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-2)
Molecular weight formula_weight	43045.0 kDa
Mutation mutation	RESIDUES 66 - 98 EXCISED
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3045

HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2. LOOP (66-98) DELETION MUTANT

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

PROTEIN (PLASMINOGEN ACTIVATOR INHIBITOR-2)

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) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
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	209

fit	/app/data/saxs_computation/by/1by7/1by7.fit
pddf	/app/data/pr_computation/by/1by7/1by7.pr.out
profile	/app/data/saxs_computation/by/1by7/1by7.dat