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- PDB-8rtn: Human thrombin in complex with a trivalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 8rtn
TitleHuman thrombin in complex with a trivalent inhibitor
Components
  • Prothrombin
  • Synthetic trivalent inhibitor
KeywordsBLOOD CLOTTING / inhibitor / tyrosine-o-sulfate
Function / homology
Function and homology information


cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway ...cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / negative regulation of proteolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / Regulation of Complement cascade / acute-phase response / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / growth factor activity / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / response to wounding / 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 / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of protein phosphorylation / positive regulation of cell growth / : / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / 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. ...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 / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Glossina morsitans morsitans (fry)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsRipoll-Rozada, J. / Maxwell, J. / Payne, R.J. / Pereira, P.J.B.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Foundation for Science and Technology (FCT)PTDC/BIA-BQM/2494/2020 Portugal
CitationJournal: To Be Published
Title: Human thrombin in complex with a trivalent inhibitor
Authors: Ripoll-Rozada, J. / Maxwell, J. / Payne, R.J. / Pereira, P.J.B.
History
DepositionJan 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Prothrombin
H: Prothrombin
I: Synthetic trivalent inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8475
Polymers145,6033
Non-polymers2442
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-39 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.188, 82.188, 271.964
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Prothrombin / Coagulation factor II


Mass: 70122.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#2: Protein/peptide Synthetic trivalent inhibitor


Mass: 5357.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Glossina morsitans morsitans (fry)
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium citrate tribasic tetrahydrate 20% (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 PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.509→68.86 Å / Num. obs: 12545 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 43.94 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.068 / Net I/σ(I): 16.9
Reflection shellResolution: 2.509→2.552 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 615 / CC1/2: 0.7 / Rpim(I) all: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→68.86 Å / SU ML: 0.2597 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.8144
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2135 665 5.3 %
Rwork0.1684 11876 -
obs0.1708 12541 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.54 Å2
Refinement stepCycle: LAST / Resolution: 2.51→68.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 0 15 117 2744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00432688
X-RAY DIFFRACTIONf_angle_d0.70013631
X-RAY DIFFRACTIONf_chiral_restr0.0481371
X-RAY DIFFRACTIONf_plane_restr0.0065477
X-RAY DIFFRACTIONf_dihedral_angle_d14.68071041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.70.28451120.22522343X-RAY DIFFRACTION100
2.7-2.970.29391350.21462342X-RAY DIFFRACTION99.96
2.97-3.410.24011360.19692347X-RAY DIFFRACTION100
3.41-4.290.20361460.14712357X-RAY DIFFRACTION99.96
4.29-68.860.17261360.14532487X-RAY DIFFRACTION99.81
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)
16.69523348327-0.441641910877-5.162876650683.23638874881.73889950415.279046293330.8234465577330.8621395191880.798717641612-0.423538425463-0.3305011435571.02671768408-1.10765083037-0.7892344069-0.2971970619640.8738119582880.136269467383-0.02036980396080.267940395437-0.1042462445060.652675048113-14.599713494137.5124351553-15.9467055785
25.98032050127-5.467416848-0.836470940288.347950266321.368694847045.93257518108-0.1580026844720.07131972563180.1171640033440.3226439668560.154631034008-1.09241747658-0.1648409403180.03099616726050.06464380780250.6749755257110.003512233150780.00545255962110.307235582699-0.1315231391060.520809628782-4.8479153507236.8301311283-7.48832014396
34.65946489173.22447672044-3.502834779274.08457701824-4.275279210914.472121511020.4613099732950.7565357309850.495383220676-0.201800227742-0.608013441552-0.802020865651-0.6645583705160.1117783848190.415525177710.574664388347-0.06160552993040.01599804072430.440071177070.04487032083850.6896003476715.2489816243135.2066779326-18.4325592288
41.17055842513-0.07485160980410.06303009359312.97258807420.2606995748722.373566276580.001468154582960.09062425752050.02393726270770.201912738049-0.1703238329150.550804446892-0.155619784783-0.4026843651330.1979916309540.3134815663040.094599934985-0.01292635375280.321517581882-0.03660765157010.447518647859-16.493800637618.2121036459-19.1088398583
52.75038948131-0.260666849093-0.4616511018574.185524897031.08550078962.94030030510.171810346774-0.5143969798380.1310506798220.682237654065-0.2995742806790.9118152332440.330847421251-0.7531218168220.2967532727060.4136533916510.0555783018030.1121349957910.429305756678-0.06009688194830.592789676891-20.952743640118.7908765084-9.11115844854
62.924273683670.2448707847870.1527981622634.226969100010.5339155628743.05547626471-0.1337256885470.4758879111860.419955780726-0.4643631658520.02941983444190.3808631823340.041599101634-0.666791788470.180728023860.3980610484650.0976144252082-0.1353953207840.3437492456670.005925346882230.430774436629-19.160123842218.9135639149-30.6690813796
73.22314976996-0.007413995997780.6259344564452.815893599661.083219622621.80341821404-0.202233924514-0.009368234128860.654154526629-0.210458525628-0.06738680722840.367545142354-0.6092681736-0.2462890396670.1196639562770.5388147674060.106587502761-0.08246716364820.248513452434-0.001903595027950.442716148861-12.562673127331.5725014928-20.7712535949
83.40209557420.511825022577-0.9341683137653.007640282240.1884037409044.37856548178-0.0987955783635-0.0934952284536-0.3034670919450.2082850436380.0259716556721-0.1747507170760.0604149564216-0.02529292982270.0312267597320.2743922338420.0364766519342-0.07792972031170.1807254178040.00142689787790.338090338703-2.4637173645717.325071891-15.6890597237
98.344127914710.2517971937290.02762282051615.95215023164-0.6049221358795.073351932940.4314253166721.432701927390.0326202844714-1.2062054767-0.157799911646-0.140083934933-0.546561873567-0.170622218059-0.2059936266180.4616875653360.02603189164430.06464042965790.433017120772-0.02292852977670.3075857150240.9362434753718.5730932786-37.0141826438
102.26802289069-0.1994668675970.09160181016694.032087677420.2752737322511.847904740690.1240919180940.2667974727680.2363784501-0.380779792045-0.150151962652-0.0166671184284-0.4465611978610.01922494785740.01961400138830.4118308933770.0299594560652-0.004711897598880.2160899254810.01784166875590.279692353824-5.7974537690325.0095318173-25.6642468325
111.301506034460.269823170698-1.896200886741.66379379872-0.4703521955072.766194008910.167462716830.2025002128010.859482436515-0.4392599321760.0442960118027-1.0213655241-1.496623250431.306122926810.1604890856570.878860670117-0.329368876740.3118850393381.065782686680.1803749809570.6964572534063.7533247606531.3615809533-33.9035266864
122.8859173710.7684494571033.201166656433.960637075910.1554951436597.21904953269-0.2967916389420.09579001426770.862415478536-0.5587122335570.05067958903770.527197923718-1.57623744592-0.3750453892340.3189585740471.270546508030.218078629098-0.02654515886990.8820703535220.04179746329310.746140158469-10.15527240832.8489039055-38.4173611213
137.21697557854-0.199152686819-2.867629855547.045353613344.076384238113.40619905303-0.7022264596180.235808419668-1.114516999-0.5272930664860.0173373718899-0.846081473740.338280527981.759335462770.6791752723370.509659847070.0483744850460.02145171949970.407138911465-0.07126023484560.441350174734-5.044251246987.97298711723-34.8656540121
143.326337537670.1467234184290.1208341253472.536325716940.1317289323042.661170534520.1555134051890.204469031759-0.6088605658660.118757774353-0.1213291309810.9897320602750.3010524335350.04229729154630.1002727823310.3099569890830.05419930540780.02573867524450.2161618498610.04242946289320.303792410435-11.27067224797.18645971788-20.0090947248
153.21596941095-1.427340288830.1515743907616.075630175982.829074136583.671038992720.447950874182-0.7170426739810.08277782130340.315934415625-0.5590093987951.424711676060.259270162182-1.202881967770.3487640303210.5421793413020.03230344683460.3057329238820.5899008920220.01967797866380.706737011564-26.12961190613.0932048271-7.71303684958
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 286 through 299 )LA286 - 2991 - 14
22chain 'L' and (resid 300 through 308 )LA300 - 30815 - 23
33chain 'L' and (resid 309 through 319 )LA309 - 31924 - 34
44chain 'H' and (resid 321 through 375 )HB321 - 3751 - 55
55chain 'H' and (resid 376 through 396 )HB376 - 39656 - 76
66chain 'H' and (resid 397 through 420 )HB397 - 42077 - 100
77chain 'H' and (resid 421 through 460 )HB421 - 460101 - 140
88chain 'H' and (resid 461 through 489 )HB461 - 489141 - 162
99chain 'H' and (resid 490 through 504 )HB490 - 504163 - 177
1010chain 'H' and (resid 505 through 578 )HB505 - 578178 - 251
1111chain 'I' and (resid 1 through 5 )ID1 - 51 - 5
1212chain 'I' and (resid 6 through 11 )ID6 - 116 - 11
1313chain 'I' and (resid 22 through 26 )ID22 - 2613 - 17
1414chain 'I' and (resid 27 through 36 )ID27 - 3618 - 27
1515chain 'I' and (resid 37 through 48 )ID37 - 4828 - 39

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