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- PDB-7phx: Tsetse thrombin inhibitor in complex with human alpha-thrombin - ... -

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Basic information

Entry
Database: PDB / ID: 7phx
TitleTsetse thrombin inhibitor in complex with human alpha-thrombin - acid-stable sulfotyrosine analogue
Components
  • Thrombin heavy chain
  • Thrombin light chain
  • Tsetse thrombin inhibitor
KeywordsBLOOD CLOTTING / anticoagulant / exosite II binding / sulfotyrosine sulfonate analogue
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
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. ...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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Tsetse thrombin inhibitor / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
Glossina morsitans morsitans (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPereira, P.J.B. / Ripoll-Rozada, J. / Calisto, B.M.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-BQM/2494/2020 Portugal
Fundacao para a Ciencia e a TecnologiaDL 57/2016/CP1355/CT0011 Portugal
CitationJournal: Chem.Commun.(Camb.) / Year: 2021
Title: Synthesis and evaluation of peptidic thrombin inhibitors bearing acid-stable sulfotyrosine analogues.
Authors: Dowman, L.J. / Agten, S.M. / Ripoll-Rozada, J. / Calisto, B.M. / Pereira, P.J.B. / Payne, R.J.
History
DepositionAug 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 27, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Thrombin light chain
H: Thrombin heavy chain
I: Tsetse thrombin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6505
Polymers37,4053
Non-polymers2442
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-28 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.700, 80.788, 85.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein/peptide , 2 types, 2 molecules LI

#1: Protein/peptide Thrombin light chain


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734
#3: Protein/peptide Tsetse thrombin inhibitor


Mass: 3528.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Glossina morsitans morsitans (fry) / References: UniProt: O97373

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Protein / Sugars , 2 types, 2 molecules H

#2: Protein Thrombin heavy chain


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 134 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.8→42.95 Å / Num. obs: 27532 / % possible obs: 96 % / Redundancy: 3.3 % / Biso Wilson estimate: 31.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.023 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1617 / CC1/2: 0.834 / Rpim(I) all: 0.34 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TKG

6tkg


Resolution: 1.8→42.95 Å / SU ML: 0.2294 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.4648
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 1336 4.86 %
Rwork0.1828 26132 -
obs0.1848 27468 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 15 133 2560
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812517
X-RAY DIFFRACTIONf_angle_d1.00543406
X-RAY DIFFRACTIONf_chiral_restr0.0632358
X-RAY DIFFRACTIONf_plane_restr0.0081441
X-RAY DIFFRACTIONf_dihedral_angle_d15.3909960
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.860.42721250.36472602X-RAY DIFFRACTION96.84
1.86-1.940.34181210.28772605X-RAY DIFFRACTION96.09
1.94-2.030.29931260.24232581X-RAY DIFFRACTION94.62
2.03-2.130.27411340.21932641X-RAY DIFFRACTION97.4
2.13-2.270.30511390.2092628X-RAY DIFFRACTION96.61
2.27-2.440.23581150.19112564X-RAY DIFFRACTION93.41
2.44-2.690.21691410.19382644X-RAY DIFFRACTION96.8
2.69-3.080.20891470.18522639X-RAY DIFFRACTION95.74
3.08-3.880.21281270.15612614X-RAY DIFFRACTION93.49
3.88-42.950.18511610.15632614X-RAY DIFFRACTION89.98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.71535302250.270796547060.3384984331114.99599953999-1.564086480252.071460100390.749560950157-0.720854788730.1251872922960.904574287372-0.09226480451040.385642309452-0.507159993057-0.220853195557-0.5857335835020.7262157548150.02227988615410.134889704310.3484873870950.02179671033860.284756827291-2.553626695888.8314439839328.3306258448
22.26153115422-0.362019420773-0.5709159070780.7793925324871.434935198042.690208635410.203014484284-0.5278314911740.2951934259420.3410017493620.317073045255-0.223868245125-0.148213097270.3767205732080.4153706311761.43249391284-0.07408160633440.1446982283170.369357307414-0.156961820.01573163204175.1097464677712.294080161730.647567558
38.847582282150.448027114924-1.156588734993.69323584038-2.863427694032.301853772910.208104878387-0.4576909729141.107577842480.457674444581-0.597620874412-0.0137475740317-1.049843128320.008047319623080.3281915545940.862520856873-0.0668742363774-0.0002271081632360.318349940856-0.09648093836570.4638598948518.6557509316420.974503626319.6765821178
41.739595658740.958112870293-1.265446939642.34307456636-0.2955657390052.73601549185-0.1228324385390.199362079654-0.221611726442-0.2519751916690.03545556566060.07976407582570.677799730042-0.1761716395520.08784812126750.629718989741-0.00792358664270.02367425479140.25038324844-0.005166287731440.2793443150810.25116493486-5.8040125288712.932703582
52.0403987090.807792626384-0.3551613982022.66336484559-0.4712285675792.891765784740.117423416949-0.0152855261790.03006980974830.225956097605-0.06232279293090.194878805988-0.1180685188290.0197989045862-0.07176731325720.5562421768180.03811949916530.06007679919180.19013115148-0.003788792135330.1980483610642.785594876815.2151504128616.6008011215
62.249535619550.734623123858-1.191270453422.52089668084-0.4545754129192.550229102150.02419121111670.2685746726850.226025730679-0.4343867499360.1202675885520.0979169232769-0.200263247883-0.00974072145809-0.1215771818410.5648587728440.0179608854310.008546994028970.220329007520.01963241374730.2041297491574.491127510149.310934463527.02736754256
72.40327749682-1.70006064013-1.560464798584.126886441311.152256374441.166690194450.3218639538380.7811620420910.130872233265-0.429434039511-0.228466048520.649427680573-0.472301632583-0.742214370314-0.1592764620650.895532971489-0.00598216091258-0.05938931231650.549525055950.1726168730010.303576828922-3.4410662246313.55495877650.0720289280918
82.595336161610.138330002217-1.768481285981.4202244169-1.301746246264.817799160980.1531522968160.0156369963552-0.0941168755301-0.283996805475-0.07120849139230.2362994669960.128769454919-0.405165782411-0.07552709366511.125416004850.03173919438360.05410379612520.4423654248890.03450713756170.27319630200910.833145439-2.09979838143-3.00466695443
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 291 through 299 )LA291 - 2991 - 9
22chain 'L' and (resid 300 through 308 )LA300 - 30810 - 18
33chain 'L' and (resid 309 through 319 )LA309 - 31919 - 29
44chain 'H' and (resid 321 through 420 )HB321 - 4201 - 100
55chain 'H' and (resid 421 through 489 )HB421 - 489101 - 162
66chain 'H' and (resid 490 through 574 )HB490 - 574163 - 247
77chain 'I' and (resid 1 through 23 )IC - E1 - 231 - 15
88chain 'I' and (resid 24 through 32 )IE24 - 3216 - 24

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