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1w7z

Crystal structure of the free (uncomplexed) Ecballium elaterium trypsin inhibitor (EETI-II)

Method: X-RAY DIFFRACTION Dmax: 59.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRYPSIN INHIBITOR II

ECBALLIUM ELATERIUM

UniProt P12071

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 homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–31 Chain B； UniProt 1–31 Chain C； UniProt 1–31 Chain D； UniProt 1–31 Chain E； UniProt 1–31 Chain F； UniProt 1–31 Not recorded NA SODIUM ION × 3 FMT FORMIC ACID × 3 X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；2M NA-FORMATE 0.1 M NA-ACETATE PH 4.6 Resolution 1.67 Å R-free 0.235
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain G； UniProt 1–31 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；2M NA-FORMATE 0.1 M NA-ACETATE PH 4.6 Resolution 1.67 Å R-free 0.235
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain H； UniProt 1–31 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；2M NA-FORMATE 0.1 M NA-ACETATE PH 4.6 Resolution 1.67 Å R-free 0.235

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 1W7Z Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1H9H COMPLEX OF EETI-II WITH PORCINE TRYPSIN Deposited 2001-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 1–30（30 aa）
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；pH 6.70
Resolution 1.50 Å R-free 0.276
1H9I COMPLEX OF EETI-II MUTANT WITH PORCINE TRYPSIN Deposited 2001-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 1–30（30 aa）
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.7；pH 6.70
Resolution 1.90 Å R-free 0.175
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 conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 16–29（14 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 conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 16–29（14 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
2ETI USE OF RESTRAINED MOLECULAR DYNAMICS IN WATER TO DETERMINE THREE-DIMENSIONAL PROTEIN STRUCTURE: PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF ECBALLIUM ELATERIUM TRYPSIN INHIBITOR II Deposited 1991-07-15 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–28（28 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2IT7 Solution structure of the squash trypsin inhibitor EETI-II Deposited 2006-10-19 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–28（28 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 2.7；285 K；Pressure 1
NMR measurement conditions pH 2.7；300 K；Pressure 1
NMR sample composition 4mM EETI-II, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 4mM EETI-II, D2O | D2O
Resolution not provided
2LET AN 1H NMR DETERMINATION OF THE THREE DIMENSIONAL STRUCTURES OF MIRROR IMAGE FORMS OF A LEU-5 VARIANT OF THE TRYPSIN INHIBITOR ECBALLIUM ELATERIUM (EETI-II) Deposited 1994-01-04 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–28（28 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ITR2_ECBEL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–31； UniProt 1–31 Author chain B； PDBConstruct 1–31； UniProt 1–31 Author chain C； PDBConstruct 1–31； UniProt 1–31 Author chain D； PDBConstruct 1–31； UniProt 1–31 Author chain E； PDBConstruct 1–31； UniProt 1–31 Author chain F； PDBConstruct 1–31； UniProt 1–31 Author chain G； PDBConstruct 1–31； UniProt 1–31 Author chain H； PDBConstruct 1–31； UniProt 1–31

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 1w7z

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1w7z
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1w7z
Deposition date deposition_date2004-09-14
Structure title titleCrystal structure of the free (uncomplexed) Ecballium elaterium trypsin inhibitor (EETI-II)
Keywords keywordsSQUASH SEED INHIBITOR, CYSTEIN KNOT, ECBALLIUM ELATERIUM, TRYPSIN, PROTEASE INHIBITOR; PROTEASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.67 Å
Radius of gyration Rg (electron density) rg_electron17.65 Å
Forward intensity I(0) i013729200.00
Molecular weight molecular_weight24663.0 kDa
Excluded volume excluded_volume29689 ų
Envelope volume envelope_volume37118 ų
Hydration-shell volume shell_volume17742 ų
Envelope diameter envelope_diameter61.7 Å
Shell Rg shell_rg23.54 Å
Envelope Rg envelope_rg17.86 Å
Shape Rg shape_rg17.69 Å
Total Rg total_rg18.42 Å
Total atoms total_atoms1678
Residues n_residues245
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 dmax59.7 Å
Rg (real space) rg_real18.56 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real1.3730e+07
I(0) uncertainty (real space) i0_real_error1.5780e+05
Rg (reciprocal space) rg_reciprocal18.58 Å
I(0) (reciprocal space) i0_reciprocal13730000.0000
Solution quality estimate total_estimate0.7181
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.5 Å
Skewness Skewness skewness0.144
Kurtosis Kurtosis kurtosis-0.272
Angular range angular_range— – 0.4250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1117000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 0.313; Positv: 1.000; Valcen: 0.991; Smooth: 0.990
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1w7za_
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
Domain ID domain_idd1w7zb_
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
Domain ID domain_idd1w7zc_
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
Domain ID domain_idd1w7zd_
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
Domain ID domain_idd1w7ze_
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
Domain ID domain_idd1w7zf_
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
Domain ID domain_idd1w7zg_
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
Domain ID domain_idd1w7zh_
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 (1)

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9. Files and Curves (10)