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- PDB-1avg: THROMBIN INHIBITOR FROM TRIATOMA PALLIDIPENNIS -

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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 / blood vessel diameter maintenance / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / : ...symbiont-mediated perturbation of host defenses / fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / blood vessel diameter maintenance / acute-phase response / serine-type endopeptidase inhibitor activity / platelet activation / : / toxin activity / 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 / 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 / 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 beta-barrel core domain / Calycin / Lipocalin / 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
Prothrombin / Triabin
Similarity search - Component
Biological speciesTriatoma pallidipennis (insect)
Bos taurus (domestic 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 (domestic 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 (domestic 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


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.
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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 %

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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

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