[English] 日本語
Yorodumi
- PDB-1adz: THE SOLUTION STRUCTURE OF THE SECOND KUNITZ DOMAIN OF TISSUE FACT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1adz
TitleTHE SOLUTION STRUCTURE OF THE SECOND KUNITZ DOMAIN OF TISSUE FACTOR PATHWAY INHIBITOR, NMR, 30 STRUCTURES
ComponentsTISSUE FACTOR PATHWAY INHIBITOR
KeywordsHYDROLASE / INHIBITOR / COAGULATION
Function / homology
Function and homology information


negative regulation of blood coagulation / Extrinsic Pathway of Fibrin Clot Formation / endopeptidase inhibitor activity / cellular response to steroid hormone stimulus / side of membrane / caveola / serine-type endopeptidase inhibitor activity / blood coagulation / cell surface / endoplasmic reticulum ...negative regulation of blood coagulation / Extrinsic Pathway of Fibrin Clot Formation / endopeptidase inhibitor activity / cellular response to steroid hormone stimulus / side of membrane / caveola / serine-type endopeptidase inhibitor activity / blood coagulation / cell surface / endoplasmic reticulum / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Tissue factor pathway inhibitor-like / 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 ...Tissue factor pathway inhibitor-like / 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
Similarity search - Domain/homology
Tissue factor pathway inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DIANA
AuthorsBurgering, M.J.M. / Orbons, L.P.M.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The second Kunitz domain of human tissue factor pathway inhibitor: cloning, structure determination and interaction with factor Xa.
Authors: Burgering, M.J. / Orbons, L.P. / van der Doelen, A. / Mulders, J. / Theunissen, H.J. / Grootenhuis, P.D. / Bode, W. / Huber, R. / Stubbs, M.T.
#1: Journal: Curr.Pharm.Des. / Year: 1996
Title: Structural Aspects of Factor Xa Inhibition
Authors: Stubbs II, M.T.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: X-Ray Structure of Active Site-Inhibited Clotting Factor Xa. Implications for Drug Design and Substrate Recognition
Authors: Brandstetter, H. / Kuhne, A. / Bode, W. / Huber, R. / Von Der Saal, W. / Wirthensohn, K. / Engh, R.A.
#3: Journal: Embo J. / Year: 1996
Title: The Ornithodorin-Thrombin Crystal Structure, a Key to the Tap Enigma?
Authors: Van De Locht, A. / Stubbs, M.T. / Bode, W. / Friedrich, T. / Bollschweiler, C. / Hoffken, W. / Huber, R.
#4: Journal: FEBS Lett. / Year: 1995
Title: Crystal Structures of Factor Xa Specific Inhibitors in Complex with Trypsin: Structural Grounds for Inhibition of Factor Xa and Selectivity Against Thrombin
Authors: Stubbs, M.T. / Huber, R. / Bode, W.
#5: Journal: J.Mol.Biol. / Year: 1993
Title: Structure of Human Des(1-45) Factor Xa at 2.2 A Resolution
Authors: Padmanabhan, K. / Padmanabhan, K.P. / Tulinsky, A. / Park, C.H. / Bode, W. / Huber, R. / Blankenship, D.T. / Cardin, A.D. / Kisiel, W.
#6: Journal: J.Mol.Biol. / Year: 1992
Title: Determination of a High-Quality Nuclear Magnetic Resonance Solution Structure of the Bovine Pancreatic Trypsin Inhibitor and Comparison with Three Crystal Structures
Authors: Berndt, K.D. / Guntert, P. / Orbons, L.P. / Wuthrich, K.
History
DepositionFeb 19, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TISSUE FACTOR PATHWAY INHIBITOR


Theoretical massNumber of molelcules
Total (without water)8,3791
Polymers8,3791
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 300LOWEST VALUE OF VARIABLE TARGET FUNCTION
Representative

-
Components

#1: Protein TISSUE FACTOR PATHWAY INHIBITOR / TFPI / EPI / LACI


Mass: 8379.239 Da / Num. of mol.: 1 / Fragment: FACTOR XA-BINDING DOMAIN (DOMAIN II) / Mutation: N-TERMINAL INS(DYKDDDDKL)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Organ: BLOOD / Plasmid: PFLAG / Production host: Escherichia coli (E. coli) / Strain (production host): JE5505 / References: UniProt: P10646

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HOMONUCLEAR NOESY
121COSY
131TOCSY

-
Sample preparation

Sample conditionspH: 4.5 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DRX600 / Manufacturer: Bruker / Model: DRX600 / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
DIANAGUNTERT,WUTHRICHrefinement
TRIAD NMR FROM TRIPOSTRIPOSstructure solution
RefinementMethod: DIANA / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE DIANA PROGRAM BUT WERE NOT FURTHER REFINED USING A FORCE FIELD AND ENERGY MINIMIZATION AND/OR MOLECULAR DYNAMICS CALCULATIONS
NMR ensembleConformer selection criteria: LOWEST VALUE OF VARIABLE TARGET FUNCTION
Conformers calculated total number: 300 / Conformers submitted total number: 30

+
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