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- PDB-7zkm: X-ray structure of the complex between human alpha thrombin and a... -

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Basic information

Entry
Database: PDB / ID: 7zkm
TitleX-ray structure of the complex between human alpha thrombin and a pseudo-cyclic thrombin binding aptamer (TBA-NNp/DDp) - Crystal form beta
Components
  • TBA-NNp/DDp
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE / Thrombin / Aptamer / Complex / Inhibitor / Coagulation
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 / 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
Chem-0G6 / Chem-JKR / Chem-JL0 / : / DNA / DNA (> 10) / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTroisi, R. / Sica, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Ther Nucleic Acids / Year: 2022
Title: A terminal functionalization strategy reveals unusual binding abilities of anti-thrombin anticoagulant aptamers.
Authors: Troisi, R. / Riccardi, C. / Perez de Carvasal, K. / Smietana, M. / Morvan, F. / Del Vecchio, P. / Montesarchio, D. / Sica, F.
History
DepositionApr 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.year
Revision 1.2Dec 14, 2022Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.country

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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
A: TBA-NNp/DDp
B: TBA-NNp/DDp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,67313
Polymers43,3634
Non-polymers4,3109
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-26 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.600, 76.600, 129.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein/peptide / Protein / DNA chain / Sugars , 4 types, 5 molecules LHAB

#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, thrombin
#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, thrombin
#3: DNA chain TBA-NNp/DDp


Mass: 4743.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 6 types, 52 molecules

#5: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-JL0 / 3-[13-methyl-5,7,12,14-tetrakis(oxidanylidene)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1(15),2,4(16),8,10-pentaen-6-yl]propyl 3-[5,7,12,14-tetrakis(oxidanylidene)-13-(3-oxidanylpropyl)-6,13-diazatetracyclo[6.6.2.0^{4,16}.0^{11,15}]hexadeca-1,3,8(16),9,11(15)-pentaen-6-yl]propyl hydrogen phosphate


Mass: 1044.737 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H43N4O21P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-JKR / 3-[5-[3-bis(oxidanyl)phosphanyloxypropoxy]naphthalen-1-yl]oxypropyl 3-(5-oxidanylnaphthalen-1-yl)oxypropyl hydrogen phosphate


Mass: 620.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H34O11P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.2 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000 20% w/v, 2-propanol 20% v/v, trisodium citrate 0.1 M, pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→59.1 Å / Num. obs: 30224 / % possible obs: 99.8 % / Redundancy: 18.1 % / CC1/2: 1 / Net I/σ(I): 23.7
Reflection shellResolution: 2→2.04 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1486 / CC1/2: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata processing
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PPB

1ppb


Resolution: 2→59.1 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.026 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 1532 5.1 %RANDOM
Rwork0.2262 ---
obs0.2275 28692 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167.9 Å2 / Biso mean: 62.661 Å2 / Biso min: 28.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20 Å2
2--0.19 Å2-0 Å2
3----0.61 Å2
Refinement stepCycle: final / Resolution: 2→59.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 562 259 44 3115
Biso mean--93.6 53.47 -
Num. residues----304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123228
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.6974506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2515276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30121.231130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14115419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9641520
X-RAY DIFFRACTIONr_chiral_restr0.1170.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022226
LS refinement shellResolution: 2.002→2.054 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 95 -
Rwork0.312 2093 -
all-2188 -
obs--100 %
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)
14.2154-0.70030.45926.1753-1.12795.4304-0.2282-0.3252-0.37540.1730.30460.99820.147-0.585-0.07640.03320.03140.07890.27530.0320.3807-31.318324.3474-23.339
23.4202-0.78930.76234.0772-0.64632.2713-0.2046-0.16610.04390.22160.1063-0.01280.027-0.02820.09840.03520.01850.01040.0321-0.01920.0347-11.828923.7664-22.2416
32.91080.5152-1.13113.85862.32836.7745-0.0785-0.37910.16610.5385-0.0219-0.0763-0.1892-0.3630.10040.6820.09970.13440.5542-0.00390.3668-23.905425.16487.6331
46.06190.5467-0.07596.6670.03842.7539-0.17880.28530.1593-0.19520.0699-0.3769-0.03310.39070.10890.31240.08950.10360.4482-0.06860.19019.564110.0202-36.6272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L7 - 103
2X-RAY DIFFRACTION2H37 - 439
3X-RAY DIFFRACTION3A1 - 201
4X-RAY DIFFRACTION4B1 - 201

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