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- PDB-1d0d: CRYSTAL STRUCTURE OF TICK ANTICOAGULANT PROTEIN COMPLEXED WITH BO... -

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Basic information

Entry
Database: PDB / ID: 1d0d
TitleCRYSTAL STRUCTURE OF TICK ANTICOAGULANT PROTEIN COMPLEXED WITH BOVINE PANCREATIC TRYPSIN INHIBITOR
Components
  • ANTICOAGULANT PROTEIN
  • PANCREATIC TRYPSIN INHIBITOR
KeywordsBLOOD CLOTTING INHIBITOR / FACTOR XA INHIBITOR / KUNITZ INHIBITOR
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
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
Similarity search - Domain/homology
Pancreatic trypsin inhibitor / Tick anticoagulant peptide
Similarity search - Component
Biological speciesOrnithodoros moubata (arthropod)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.62 Å
AuthorsSt.Charles, R. / Padmanabhan, K. / Arni, R.V. / Padmanabhan, K.P. / Tulinsky, A.
CitationJournal: Protein Sci. / Year: 2000
Title: Structure of tick anticoagulant peptide at 1.6 A resolution complexed with bovine pancreatic trypsin inhibitor.
Authors: St.Charles, R. / Padmanabhan, K. / Arni, R.V. / Padmanabhan, K.P. / Tulinsky, A.
History
DepositionSep 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Database references / Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Oct 11, 2017Group: Data collection / Category: reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.6Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.7Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.8Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.9Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTICOAGULANT PROTEIN
B: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8085
Polymers13,5202
Non-polymers2883
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.87, 46.87, 50.35
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein ANTICOAGULANT PROTEIN / TAP


Mass: 6992.614 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ornithodoros moubata (arthropod) / References: UniProt: P17726
#2: Protein PANCREATIC TRYPSIN INHIBITOR / BPTI


Mass: 6527.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00974
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.1 MADA1reservoir
31.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 8, 1993
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.62→47 Å / Num. all: 14018 / Num. obs: 13056 / Observed criterion σ(F): 0.5 / Observed criterion σ(I): 1 / Redundancy: 6.6 % / Biso Wilson estimate: 22.8 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.8
Reflection shellResolution: 1.62→1.88 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.336 / Num. unique all: 3807
Reflection
*PLUS
% possible obs: 93.1 % / Num. measured all: 86488
Reflection shell
*PLUS
% possible obs: 88.4 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 3.9

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementResolution: 1.62→8 Å / σ(F): 1 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.211 665 random
Rwork0.189 --
all0.19 12942 -
obs0.19 12942 -
Refinement stepCycle: LAST / Resolution: 1.62→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 15 124 1082
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 1 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.5

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