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2kmp

Solution structure of intermeidate IIa of Leeck-derived tryptase inhibitor, LDTI.

Method: SOLUTION NMR Dmax: 26.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Leech-derived tryptase inhibitor C

Hirudo medicinalis

UniProt P80424

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 1–44 Fragment：residues 1-44 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 1.7；298 K；Pressure ambient NMR sample composition：1.7 mM LDTI, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：1.7 mM LDTI, 100% D2O | 100% 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 2KMP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AN1 LEECH-DERIVED TRYPTASE INHIBITOR/TRYPSIN COMPLEX Deposited 1997-06-26 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 I 1–46（46 aa）
Mutation：N115D (D-ASPARTIC ACID FORM) CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；30% V/V 2-PROPANOL, 0.2M AMMONIUM ACETATE, 0.1M TRIS-HCL, PH 8.5 ROOM TEMPERATURE 27 MONTHS FOR GROWTH.
Resolution 2.03 Å R-free 0.228
1LDT COMPLEX OF LEECH-DERIVED TRYPTASE INHIBITOR WITH PORCINE TRYPSIN Deposited 1997-05-15 Different construct 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 L 1–46（46 aa）
Not recorded CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；10% PEG 6000, 2.3M PHOSPHATE, PH 8.0
Resolution 1.90 Å
2KMO Solution structure of native Leech-derived tryptase inhibitor, LDTI Deposited 2009-08-03 Parsed fields agree Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–44（44 aa） Fragment：residues 1-44
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 1.7；298 K；Pressure ambient
NMR sample composition 1.7 mM LDTI, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.7 mM LDTI, 100% D2O | 100% D2O
Resolution not provided
2KMQ Solution structure of intermediate IIb of Leech-derived tryptase inhibitor, LDTI. Deposited 2009-08-03 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–44（44 aa） Fragment：residues 1-44
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 1.7；298 K；Pressure ambient
NMR sample composition 1.7 mM LDTI-IIb, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.7 mM LDTI-IIb, 100% D2O | 100% D2O
Resolution not provided
2KMR Solution structure of intermediate IIc of Leech-derived tryptase inhibitor, LDTI. Deposited 2009-08-03 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–44（44 aa） Fragment：residues 1-44
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 1.7；298 K；Pressure ambient
NMR sample composition 1.7 mM LDTI-IIc, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 1.7 mM LDTI-IIc, 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 LDTI_HIRME
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–44； UniProt 1–44

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 2kmp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2kmp
Deposition date deposition_date2009-08-03
Structure title titleSolution structure of intermeidate IIa of Leeck-derived tryptase inhibitor, LDTI.
Keywords keywordsDisulfide bond, Protease inhibitor, Serine protease inhibitor, HYDROLASE; HYDROLASE
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier10.44 Å
Radius of gyration Rg (electron density) rg_electron11.14 Å
Forward intensity I(0) i0132573000.00
Molecular weight molecular_weight90428.0 kDa
Excluded volume excluded_volume111340 ų
Envelope volume envelope_volume16231 ų
Hydration-shell volume shell_volume9985 ų
Envelope diameter envelope_diameter53.7 Å
Shell Rg shell_rg19.53 Å
Envelope Rg envelope_rg15.62 Å
Shape Rg shape_rg11.07 Å
Total Rg total_rg11.68 Å
Total atoms total_atoms12600
Residues n_residues880
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 dmax26.9 Å
Rg (real space) rg_real9.77 Å
Rg uncertainty (real space) rg_real_error0.04 Å
I(0) (real space) i0_real1.2650e+08
I(0) uncertainty (real space) i0_real_error9.4980e+05
Rg (reciprocal space) rg_reciprocal10.58 Å
I(0) (reciprocal space) i0_reciprocal132600000.0000
Solution quality estimate total_estimate0.6851
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary11.9 Å
Skewness Skewness skewness0.239
Kurtosis Kurtosis kurtosis-0.494
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha3.8140
Highest regularization parameter α highest_alpha22120.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.002; Oscil: 0.998; Stabil: 0.974; Sysdev: 0.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000
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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2kmpa_
Class classg — Small proteins
Fold Fold foldg.68 — Kazal-type serine protease inhibitors
Superfamily Superfamily superfamilyg.68.1 — Kazal-type serine protease inhibitors
Family Family familyg.68.1.1 — Ovomucoid domain III-like

CATH v4.4 (1 domains)

Domain ID domain_id2kmpA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily30 —
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8. Citations (1)

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9. Files and Curves (10)