[English] 日本語
Yorodumi
- PDB-1ldt: COMPLEX OF LEECH-DERIVED TRYPTASE INHIBITOR WITH PORCINE TRYPSIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ldt
TitleCOMPLEX OF LEECH-DERIVED TRYPTASE INHIBITOR WITH PORCINE TRYPSIN
Components
  • TRYPSIN
  • TRYPTASE INHIBITOR
KeywordsCOMPLEX (HYDROLASE/INHIBITOR) / COMPLEX (HYDROLASE-INHIBITOR) / HYDROLASE / INHIBITOR / INFLAMMATION / TRYPTASE / COMPLEX (HYDROLASE-INHIBITOR) complex
Function / homology
Function and homology information


trypsin / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site ...Kazal serine protease inhibitors family signature. / Kazal-type serine protease inhibitor domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #30 / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Trypsin / Leech-derived tryptase inhibitor C
Similarity search - Component
Biological speciesHirudo medicinalis (medicinal leech)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStubbs, M.T.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: The three-dimensional structure of recombinant leech-derived tryptase inhibitor in complex with trypsin. Implications for the structure of human mast cell tryptase and its inhibition.
Authors: Stubbs, M.T. / Morenweiser, R. / Sturzebecher, J. / Bauer, M. / Bode, W. / Huber, R. / Piechottka, G.P. / Matschiner, G. / Sommerhoff, C.P. / Fritz, H. / Auerswald, E.A.
#1: Journal: FEBS Lett. / Year: 1994
Title: Structure of Leech Derived Tryptase Inhibitor (Ldti-C) in Solution
Authors: Muhlhahn, P. / Czisch, M. / Morenweiser, R. / Habermann, B. / Engh, R.A. / Sommerhoff, C.P. / Auerswald, E.A. / Holak, T.A.
#2: Journal: Biol.Chem.Hoppe-Seyler / Year: 1994
Title: Recombinant Leech-Derived Tryptase Inhibitor: Construction, Production, Protein Chemical Characterization and Inhibition of HIV-1 Replication
Authors: Auerswald, E.A. / Morenweiser, R. / Sommerhoff, C.P. / Piechottka, G.P. / Eckerskorn, C. / Gurtler, L.G. / Fritz, H.
#3: Journal: Biol.Chem.Hoppe-Seyler / Year: 1994
Title: A Kazal-Type Inhibitor of Human Mast Cell Tryptase: Isolation from the Medical Leech Hirudo Medicinalis, Characterization, and Sequence Analysis
Authors: Sommerhoff, C.P. / Sollner, C. / Mentele, R. / Piechottka, G.P. / Auerswald, E.A. / Fritz, H.
History
DepositionMay 15, 1997Processing site: BNL
Revision 1.0May 20, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
T: TRYPSIN
L: TRYPTASE INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2843
Polymers28,2442
Non-polymers401
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.400, 63.400, 131.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11L-45-

LEU

-
Components

#1: Protein TRYPSIN


Mass: 23493.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: BEAN / References: UniProt: P00761, trypsin
#2: Protein/peptide TRYPTASE INHIBITOR / LDTI


Mass: 4750.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: LEECH-DERIVED TRYPTASE INHIBITOR / Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): S-78 / References: UniProt: P80424
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS STRUCTURE OF LDTI IN COMPLEX WITH TRYPSIN REVEALS STRUCTURAL ASPECTS OF THE MAST CELL ...THIS STRUCTURE OF LDTI IN COMPLEX WITH TRYPSIN REVEALS STRUCTURAL ASPECTS OF THE MAST CELL PROTEINASE TRYPTASE. THE BASIC AMINO TERMINUS, FLEXIBLE IN NMR MEASUREMENTS, APPROACHES THE 148-LOOP OF TRYPSIN, WHICH HAS AN ACIDIC COUNTERPART IN TRYPTASE. THE SIDE CHAIN OF TRYPSIN T 217 SWINGS OUT TO ACCOMMODATE THE N-TERMINAL RESIDUES.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growpH: 8 / Details: 10% PEG 6000, 2.3M PHOSPHATE, PH 8.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMMops1drop
320 mM1dropNaCl
410 %PEG60001reservoir
52.3 Mphosphate1reservoir

-
Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 21466 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 9
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4 / Rsym value: 0.2 / % possible all: 87.6
Reflection
*PLUS
Num. measured all: 139563
Reflection shell
*PLUS
% possible obs: 87.6 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PORCINE TRYPSIN MODEL FROM TRYPSIN:MUNG BEAN INHIBITOR (LIN ET AL., EUR. J. BIOCHEM. 212, 549-555 (1993)

Resolution: 1.9→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 0
Details: THE LDTI MOIETY IS WELL DEFINED IN THE VICINITY OF THE PROTEINASE, BUT IS CHARACTERIZED BY ELEVATED TEMPERATURE FACTORS AND DISRUPTED DENSITY FURTHER AWAY FROM TRYPSIN. IN PARTICULAR, AMINO ...Details: THE LDTI MOIETY IS WELL DEFINED IN THE VICINITY OF THE PROTEINASE, BUT IS CHARACTERIZED BY ELEVATED TEMPERATURE FACTORS AND DISRUPTED DENSITY FURTHER AWAY FROM TRYPSIN. IN PARTICULAR, AMINO ACID RESIDUES LYS L 1I - LYS L 2I, GLY L 15 I - ARG L 19I, SER L 33I - SER L 36I AND THE C-TERMINAL RESIDUES PRO L 41I - ASN L 46I ARE DEFINED BY EITHER WEAK OR NO ELECTRON DENSITY. ACCORDINGLY, THE COORDINATES FOR PRO L 41I - ASN L 46I ARE NOT RELIABLE.
RfactorNum. reflection% reflection
Rwork0.197 --
obs0.197 21466 98.2 %
Refine analyzeLuzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 1 149 1996
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.81
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.29 661 -
obs--63.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31
LS refinement shell
*PLUS
Rfactor obs: 0.29

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more