[English] 日本語
Yorodumi
- PDB-1avg: THROMBIN INHIBITOR FROM TRIATOMA PALLIDIPENNIS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1avg
TitleTHROMBIN INHIBITOR FROM TRIATOMA PALLIDIPENNIS
Components
  • (THROMBIN) x 2
  • TRIABIN
KeywordsCOMPLEX (BLOOD COAGULATION/INHIBITOR) / BOVINE THROMBIN / THROMBIN INHIBITOR / COMPLEX (BLOOD COAGULATION-INHIBITOR) / COMPLEX (BLOOD COAGULATION-INHIBITOR) complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / blood coagulation / collagen-containing extracellular matrix ...symbiont-mediated perturbation of host defenses / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / blood coagulation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
Similarity search - Function
Triabin/Procalin / Triabin / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Calycin beta-barrel core domain / Kringle domain ...Triabin/Procalin / Triabin / Epsilon-Thrombin; Chain L / Thrombin light chain domain / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Calycin beta-barrel core domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Kringle-like fold / Calycin / Lipocalin / Few Secondary Structures / Irregular / 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 / Mainly Beta
Similarity search - Domain/homology
Prothrombin / Triabin
Similarity search - Component
Biological speciesTriatoma pallidipennis (insect)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFuentes-Prior, P. / Huber, R. / Bode, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Structure of the thrombin complex with triabin, a lipocalin-like exosite-binding inhibitor derived from a triatomine bug.
Authors: Fuentes-Prior, P. / Noeske-Jungblut, C. / Donner, P. / Schleuning, W.D. / Huber, R. / Bode, W.
History
DepositionSep 16, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: THROMBIN
H: THROMBIN
I: TRIABIN


Theoretical massNumber of molelcules
Total (without water)50,6043
Polymers50,6043
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.840, 67.230, 183.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide THROMBIN /


Mass: 4792.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: BOVINE THROMBIN WAS PURIFIED FROM FROM FRESH OX BLOOD ACCORDING TO REPORTED PROTOCOLS
Source: (natural) Bos taurus (cattle) / Organ: BLOOD / Secretion: BLOOD / Tissue: BLOOD / References: UniProt: P00735, thrombin
#2: Protein THROMBIN /


Mass: 29772.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: BOVINE THROMBIN WAS PURIFIED FROM FROM FRESH OX BLOOD ACCORDING TO REPORTED PROTOCOLS
Source: (natural) Bos taurus (cattle) / Organ: BLOOD / Secretion: BLOOD / Tissue: BLOOD / References: UniProt: P00735, thrombin
#3: Protein TRIABIN


Mass: 16039.603 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triatoma pallidipennis (insect) / Organ: BLOOD / Production host: INSECT CELLS / References: UniProt: Q27049
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Compound detailsARG 15 A IS INSERTED IN THE ACTIVE SITE OF A NEIGHBORING MOLECULE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 4.6
Details: 50 MM NA ACETATE, PH 4.6, 100 MM (NH4)2SO4, 16 % PEG 4,000
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 mg/mlprotein1drop
250 mMNa acetate1drop
3100 mMammonium sulfate1drop
40.01 %1dropNaN3
58 %PEG40001drop
616 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→19.92 Å / Num. obs: 16392 / % possible obs: 93.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.099 / Rsym value: 0.112 / Net I/σ(I): 14.22
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.121 / Mean I/σ(I) obs: 2.65 / Rsym value: 0.148 / % possible all: 81.6
Reflection
*PLUS
Num. measured all: 79890
Reflection shell
*PLUS
% possible obs: 81.6 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
Agrovatadata reduction
AMoREphasing
X-PLOR3.842refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BOVINE THROMBIN

Resolution: 2.6→10 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.275 -5 %RANDOM
Rwork0.184 ---
obs0.184 14627 93.2 %-
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 0 172 4476
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_deg1.49
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.92
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
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
Software
*PLUS
Name: X-PLOR / Version: 3.842 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

+
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