[English] 日本語
Yorodumi
- PDB-2ra3: Human cationic trypsin complexed with bovine pancreatic trypsin i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ra3
TitleHuman cationic trypsin complexed with bovine pancreatic trypsin inhibitor (BPTI)
Components
  • Pancreatic trypsin inhibitor
  • Trypsin-1
Keywordshydrolase/hydrolase inhibitor / Human cationic trypsin / Serine protease / Bovine pancreatic trypsin inhibitor / BPTI / Calcium / Digestion / Disease mutation / Hydrolase / Metal-binding / Secreted / Sulfation / Zymogen / Pharmaceutical / Protease inhibitor / Serine protease inhibitor / hydrolase-hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / Developmental Lineage of Pancreatic Acinar Cells / molecular function inhibitor activity / Activation of Matrix Metalloproteinases ...Uptake of dietary cobalamins into enterocytes / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / Developmental Lineage of Pancreatic Acinar Cells / molecular function inhibitor activity / Activation of Matrix Metalloproteinases / negative regulation of thrombin-activated receptor signaling pathway / extracellular matrix disassembly / trypsin / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / : / protease binding / blood microparticle / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / metal ion binding
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / : / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Mainly Beta
Similarity search - Domain/homology
Pancreatic trypsin inhibitor / Serine protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsSalameh, M.A. / Soares, A.S. / Radisky, E.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural Basis for Accelerated Cleavage of Bovine Pancreatic Trypsin Inhibitor (BPTI) by Human Mesotrypsin.
Authors: Salameh, M.A. / Soares, A.S. / Hockla, A. / Radisky, E.S.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trypsin-1
B: Trypsin-1
I: Pancreatic trypsin inhibitor
C: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,64530
Polymers61,2594
Non-polymers2,38626
Water11,584643
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Trypsin-1
C: Pancreatic trypsin inhibitor
hetero molecules

A: Trypsin-1
C: Pancreatic trypsin inhibitor
hetero molecules

B: Trypsin-1
I: Pancreatic trypsin inhibitor
hetero molecules

B: Trypsin-1
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,29060
Polymers122,5198
Non-polymers4,77152
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation6_544-x+1/2,-y-1/2,z-1/21
crystal symmetry operation8_445x-1/2,-y-1/2,-z1
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area23350 Å2
ΔGint-746.2 kcal/mol
Surface area40830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.183, 186.546, 90.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-340-

HOH

-
Components

#1: Protein Trypsin-1 / Trypsin I / Cationic trypsinogen / Serine protease 1


Mass: 24102.154 Da / Num. of mol.: 2 / Mutation: R117H, S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRSS1, TRP1, TRY1, TRYP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P07477, trypsin
#2: Protein Pancreatic trypsin inhibitor / Basic protease inhibitor / BPI / BPTI / Aprotinin


Mass: 6527.568 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Strain: A1153 / References: UniProt: P00974
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris hydrochloride pH 8.5, 1.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 27, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.46→26.144 Å / Num. obs: 115118 / % possible obs: 87.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 17.335 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 19.5
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.465 / % possible all: 46.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1TRN and 2PTC

1trn

2ptc


Resolution: 1.46→26.13 Å / Isotropic thermal model: anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1777 11506 -Random
Rwork0.153 ---
obs0.1539 115064 86.8 %-
all-115064 --
Displacement parametersBiso mean: 16.36 Å2
Refinement stepCycle: LAST / Resolution: 1.46→26.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 127 665 5248
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_bond_d_na
X-RAY DIFFRACTIONf_bond_d_prot
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_angle_d_na
X-RAY DIFFRACTIONf_angle_d_prot
X-RAY DIFFRACTIONf_angle_deg0.793
X-RAY DIFFRACTIONf_angle_deg_na
X-RAY DIFFRACTIONf_angle_deg_prot
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_dihedral_angle_d_na
X-RAY DIFFRACTIONf_dihedral_angle_d_prot
X-RAY DIFFRACTIONf_improper_angle_d
X-RAY DIFFRACTIONf_improper_angle_d_na
X-RAY DIFFRACTIONf_improper_angle_d_prot
X-RAY DIFFRACTIONf_mcbond_it
X-RAY DIFFRACTIONf_mcangle_it
X-RAY DIFFRACTIONf_scbond_it
X-RAY DIFFRACTIONf_scangle_it

+
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://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