SAXSdb — 1ib9

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

TRYPSIN INHIBITOR II

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 1–34	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 3.5；293 K；Pressure ambient NMR sample composition：1 mM MCoTI-II, 90% H2O, 10% D2O \| 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 1IB9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HA9 SOLUTION STRUCTURE OF THE SQUASH TRYPSIN INHIBITOR MCoTI-II, NMR, 30 STRUCTURES. Deposited 2001-04-02	Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–34（34 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3.4；290 K；Pressure 1 NMR measurement conditions 305 K NMR sample composition 2.5MM MCOTI-II	Resolution not provided
2C4B Inhibitor cystine knot protein McoEeTI fused to the catalytically inactive barnase mutant H102A Deposited 2005-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–21（16 aa）	Mutation：YES	2PE NONAETHYLENE GLYCOL × 2 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 4 FMT FORMIC ACID × 2 SO4 SULFATE ION × 7 UNX UNKNOWN LIGAND × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.3 M AMMONIUM SULPHATE, 7% PEG400 (V/V), 0.1 M MES PH 6.5 AS RESERVOIR SOLUTION. DROPLETS MIXED FROM 8 UL PROTEIN (30 MG/ML) AND 4 UL RESERVOIR. SITTING DROP VAPOR DIFFUSION. 4 DEG. C.	Resolution 1.30 Å R-free 0.164
2C4B Inhibitor cystine knot protein McoEeTI fused to the catalytically inactive barnase mutant H102A Deposited 2005-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 6–21（16 aa）	Mutation：YES	2PE NONAETHYLENE GLYCOL × 2 EDO 1,2-ETHANEDIOL × 6 FMT FORMIC ACID × 1 SO4 SULFATE ION × 10 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1.3 M AMMONIUM SULPHATE, 7% PEG400 (V/V), 0.1 M MES PH 6.5 AS RESERVOIR SOLUTION. DROPLETS MIXED FROM 8 UL PROTEIN (30 MG/ML) AND 4 UL RESERVOIR. SITTING DROP VAPOR DIFFUSION. 4 DEG. C.	Resolution 1.30 Å R-free 0.164
2IT8 Solution structure of a linear analog of the cyclic squash trypsin inhibitor MCoTI-II Deposited 2006-10-19	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–34（29 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3；285 K；Pressure 1 NMR measurement conditions pH 3；300 K；Pressure 1 NMR sample composition 1.2 mM peptide, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.2 mM peptide, D2O \| D2O	Resolution not provided
2PO8 The structure of a two-disulfide intermediate of MCoTI-II Deposited 2007-04-26	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 8–34（27 aa） Chain A 1–7（7 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 2；298 K；Pressure atmospheric NMR sample composition 0.6 mM peptide, 0.1% TFA, pH 2, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
4GUX Crystal structure of trypsin:MCoTi-II complex Deposited 2012-08-30	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–34（34 aa）	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；28% PEG3350, 0.24M ammonium acetate, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.194
4GUX Crystal structure of trypsin:MCoTi-II complex Deposited 2012-08-30	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–34（34 aa）	Not recorded	CA CALCIUM ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；28% PEG3350, 0.24M ammonium acetate, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.194
4GUX Crystal structure of trypsin:MCoTi-II complex Deposited 2012-08-30	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–34（34 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；28% PEG3350, 0.24M ammonium acetate, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.194

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ITR2_MOMCO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–34； UniProt 1–34

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	1ib9
Deposition date deposition_date	2001-03-28
Structure title title	SOLUTION STRUCTURE OF MCOTI-II, A MACROCYCLIC TRYPSIN INHIBITOR
Keywords keywords	Cyclic cystine knot, cyclotide, circular protein, beta-hairpin, PLANT PROTEIN; PLANT PROTEIN
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	7.72 Å
Radius of gyration Rg (electron density) rg_electron	8.28 Å
Forward intensity I(0) i0	93301500.00
Molecular weight molecular_weight	69261.0 kDa
Excluded volume excluded_volume	82249 Å³
Envelope volume envelope_volume	7903 Å³
Hydration-shell volume shell_volume	6985 Å³
Envelope diameter envelope_diameter	33.1 Å
Shell Rg shell_rg	15.17 Å
Envelope Rg envelope_rg	10.51 Å
Shape Rg shape_rg	8.32 Å
Total Rg total_rg	8.39 Å
Total atoms total_atoms	9240
Residues n_residues	680
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	29.9 Å
Rg (real space) rg_real	7.71 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	9.3300e+07
I(0) uncertainty (real space) i0_real_error	9.6720e+05
Rg (reciprocal space) rg_reciprocal	7.71 Å
I(0) (reciprocal space) i0_reciprocal	93300000.0000
Solution quality estimate total_estimate	0.8009
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	9.8 Å
Skewness Skewness skewness	0.348
Kurtosis Kurtosis kurtosis	0.091
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18640.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.538; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.965

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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) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1ib9a_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.2 — Plant inhibitors of proteinases and amylases
Family Family family	g.3.2.1 — Plant inhibitors of proteinases and amylases

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8. Citations (1)

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Description description	TRYPSIN INHIBITOR II
Molecular weight formula_weight	3483.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	9240

fit	/app/data/saxs_computation/ib/1ib9/1ib9.fit
pddf	/app/data/pr_computation/ib/1ib9/1ib9.pr.out
profile	/app/data/saxs_computation/ib/1ib9/1ib9.dat

SOLUTION STRUCTURE OF MCOTI-II, A MACROCYCLIC TRYPSIN INHIBITOR

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

TRYPSIN INHIBITOR II

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)