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2it8

Solution structure of a linear analog of the cyclic squash trypsin inhibitor MCoTI-II

Method: SOLUTION NMR Dmax: 22.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Trypsin inhibitor 2

OrganismNot specified

UniProt P82409

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 6–34 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer 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

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 2IT8 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 construct Different mutation/modification 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
1IB9 SOLUTION STRUCTURE OF MCOTI-II, A MACROCYCLIC TRYPSIN INHIBITOR Deposited 2001-03-28 Different construct Different mutation/modification 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 3.5；293 K；Pressure ambient
NMR sample composition 1 mM MCoTI-II, 90% H2O, 10% D2O | 90% H2O/10% D2O
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
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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 1–29； UniProt 6–34

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2it8

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2it8
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2it8
Deposition date deposition_date2006-10-19
Structure title titleSolution structure of a linear analog of the cyclic squash trypsin inhibitor MCoTI-II
Keywords keywordsPLANT PROTEIN ANALOG, KNOTTIN, CYSTINE-KNOT, 3-10 HELIX, TRIPLE-STRANDED ANTI-PARALLEL BETA-SHEET, PLANT PROTEIN; PLANT PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier7.46 Å
Radius of gyration Rg (electron density) rg_electron8.22 Å
Forward intensity I(0) i0155142000.00
Molecular weight molecular_weight92301.0 kDa
Excluded volume excluded_volume110930 ų
Envelope volume envelope_volume6624 ų
Hydration-shell volume shell_volume6178 ų
Envelope diameter envelope_diameter34.1 Å
Shell Rg shell_rg14.66 Å
Envelope Rg envelope_rg10.30 Å
Shape Rg shape_rg8.24 Å
Total Rg total_rg8.29 Å
Total atoms total_atoms12570
Residues n_residues870
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax22.8 Å
Rg (real space) rg_real7.52 Å
Rg uncertainty (real space) rg_real_error0.04 Å
I(0) (real space) i0_real1.5360e+08
I(0) uncertainty (real space) i0_real_error1.0590e+06
Rg (reciprocal space) rg_reciprocal7.47 Å
I(0) (reciprocal space) i0_reciprocal155100000.0000
Solution quality estimate total_estimate0.6847
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary8.9 Å
Skewness Skewness skewness0.308
Kurtosis Kurtosis kurtosis-0.334
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha6.9480
Highest regularization parameter α highest_alpha5443.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.978; Stabil: 0.949; Sysdev: 0.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.131
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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_idd2it8a1
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.2 — Plant inhibitors of proteinases and amylases
Family Family familyg.3.2.1 — Plant inhibitors of proteinases and amylases
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8. Citations (3)

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9. Files and Curves (10)