SAXSdb — 1fyb

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

PROTEINASE INHIBITOR

Nicotiana alata

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 54–164	Fragment：DOMAINS 1 AND 2 (C1 AND T1) FROM THE SIX-DOMAIN PRECURSOR PROTEIN NA-PROPI	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 5.8；313 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR measurement conditions：pH 5.8；313 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR measurement conditions：pH 5.8；313 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition：1mM C1-T1, unlabeled \| 90% H2O/10% D2O NMR sample composition：1mM C1-T1, unlabeled \| 99% D2O NMR sample composition：1mM C1-T1, U-15N,13C \| 90% H2O/10% D2O	Resolution not provided

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 1FYB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CE3 PUTATIVE ANCESTRAL PROTEIN ENCODED BY A SINGLE SEQUENCE REPEAT OF THE MULTIDOMAIN PROTEINASE INHIBITOR FROM NICOTIANA ALATA Deposited 1999-03-14	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 29–82（54 aa） Fragment：FIRST SEQUENCE REPEAT	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；313 K；Pressure 1 NMR sample composition 1 mM peptide \| 90% H2O/10% D2O	Resolution not provided
1QH2 CHYMOTRYPSIN INHIBITOR (C2) FROM NICOTIANA ALATA Deposited 1999-05-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–47（18 aa） Chain B 345–372（28 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.2；313 K NMR sample composition 10% D2O/90% H2O	Resolution not provided
1TIH TRYPSIN INHIBITOR (T1) FROM NICOTIANA ALATA Deposited 1995-08-03	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 112–164（53 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1VTP VACUOLAR TARGETING PEPTIDE FROM NA-PROPI Deposited 1995-11-14	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 256–281（26 aa） Fragment：C-TERMINAL RESIDUES 29 - 54	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2JYY Solution structure of C8A/C37A-T1 from Nicotiana alata Deposited 2007-12-20	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 112–164（53 aa） Fragment：UNP residues 112-164	Mutation：C8A, C37A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.13 mM C8A/C37A-T1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.13 mM C8A/C37A-T1, 100% D2O \| 100% D2O	Resolution not provided

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q40378_NICAL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–111； UniProt 54–164

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	1fyb
Deposition date deposition_date	2000-09-28
Structure title title	SOLUTION STRUCTURE OF C1-T1, A TWO-DOMAIN PROTEINASE INHIBITOR DERIVED FROM THE CIRCULAR PRECURSOR PROTEIN NA-PROPI FROM NICOTIANA ALATA
Keywords keywords	two-domain protein, Hydrolase Inhibitor; Hydrolase Inhibitor
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	23.70 Å
Radius of gyration Rg (electron density) rg_electron	23.51 Å
Forward intensity I(0) i0	1072980000.00
Molecular weight molecular_weight	241670.0 kDa
Excluded volume excluded_volume	289640 Å³
Envelope volume envelope_volume	152700 Å³
Hydration-shell volume shell_volume	41986 Å³
Envelope diameter envelope_diameter	103.3 Å
Shell Rg shell_rg	37.77 Å
Envelope Rg envelope_rg	29.91 Å
Shape Rg shape_rg	23.50 Å
Total Rg total_rg	24.10 Å
Total atoms total_atoms	32060
Residues n_residues	2220
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	92.2 Å
Rg (real space) rg_real	23.78 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	1.0730e+09
I(0) uncertainty (real space) i0_real_error	1.5130e+07
Rg (reciprocal space) rg_reciprocal	23.77 Å
I(0) (reciprocal space) i0_reciprocal	1073000000.0000
Solution quality estimate total_estimate	0.8114
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.1 Å
Skewness Skewness skewness	0.297
Kurtosis Kurtosis kurtosis	-0.297
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	478100.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.649; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.606; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1fyba1
Class class	g — Small proteins
Fold Fold fold	g.69 — Plant proteinase inhibitors
Superfamily Superfamily superfamily	g.69.1 — Plant proteinase inhibitors
Family Family family	g.69.1.1 — Plant proteinase inhibitors

Domain ID domain_id	d1fyba2
Class class	g — Small proteins
Fold Fold fold	g.69 — Plant proteinase inhibitors
Superfamily Superfamily superfamily	g.69.1 — Plant proteinase inhibitors
Family Family family	g.69.1.1 — Plant proteinase inhibitors

CATH v4.4 (2 domains)

Domain ID domain_id	1fybA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	1fybA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	PROTEINASE INHIBITOR
Molecular weight formula_weight	12099.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	32060

来源生物 organism	Nicotiana alata
通用名 common_name	Persian tobacco
NCBI Class编号 ncbi_taxonomy_id	4087
宿主生物 host_organism	Escherichia coli

SOLUTION STRUCTURE OF C1-T1, A TWO-DOMAIN PROTEINASE INHIBITOR DERIVED FROM THE CIRCULAR PRECURSOR PROTEIN NA-PROPI FROM NICOTIANA ALATA

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

PROTEINASE INHIBITOR

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/fy/1fyb/1fyb.fit
pddf	/app/data/pr_computation/fy/1fyb/1fyb.pr.out
profile	/app/data/saxs_computation/fy/1fyb/1fyb.dat