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- PDB-6t57: Thrombin in Complex with a D-Phe-Pro-N-amidinopiperidine Derivative -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6t57
TitleThrombin in Complex with a D-Phe-Pro-N-amidinopiperidine Derivative
Components
  • (ProthrombinThrombin) x 2
  • Hirudin variant-2
KeywordsHYDROLASE / COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / SERINE PROTEASE / PROTEASE / THROMBIN INHIBITOR
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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / 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 / Golgi lumen / positive regulation of protein localization to nucleus / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle ...Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / 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-J3I / PHOSPHATE ION / trifluoroacetic acid / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsNgo, K. / Abazi, N. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Thrombin in Complex with a D-Phe-Pro-N-amidinopiperidine Derivative
Authors: Ngo, K. / Abazi, N. / Heine, A. / Klebe, G.
History
DepositionOct 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Prothrombin
H: Prothrombin
I: Hirudin variant-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,32310
Polymers35,3683
Non-polymers9557
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-36 kcal/mol
Surface area12330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.290, 71.660, 73.245
Angle α, β, γ (deg.)90.000, 100.679, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11H-403-

HOH

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Components

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Protein/peptide , 2 types, 2 molecules LI

#1: Protein/peptide Prothrombin / Thrombin / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide Hirudin variant-2


Mass: 1491.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945

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Protein / Sugars , 2 types, 2 molecules H

#2: Protein Prothrombin / Thrombin / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#7: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 , 6 types, 161 molecules

#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-J3I / (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(1-carbamimidoylpiperidin-4-yl)methyl]pyrrolidine-2-carboxamide


Mass: 400.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N6O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20 mM NaH2PO4, 350 mM NaCl, 27% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.568→43.735 Å / Num. obs: 48242 / % possible obs: 96.3 % / Redundancy: 3.52 % / Biso Wilson estimate: 23.9 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.049 / Rsym value: 0.042 / Net I/σ(I): 15.03
Reflection shellResolution: 1.57→1.66 Å / Mean I/σ(I) obs: 2.28 / Num. unique obs: 7633 / CC1/2: 0.856 / Rrim(I) all: 0.567 / Rsym value: 0.482

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UE7

4ue7


Resolution: 1.57→43.73 Å / SU ML: 0.1915 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.462
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 2411 5 %
Rwork0.1926 45815 -
obs0.1936 48226 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.77 Å2
Refinement stepCycle: LAST / Resolution: 1.57→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 61 155 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662448
X-RAY DIFFRACTIONf_angle_d0.88833321
X-RAY DIFFRACTIONf_chiral_restr0.057346
X-RAY DIFFRACTIONf_plane_restr0.0058434
X-RAY DIFFRACTIONf_dihedral_angle_d17.3541473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.60.34681330.32832543X-RAY DIFFRACTION92.18
1.6-1.630.321420.29522685X-RAY DIFFRACTION96.25
1.63-1.670.28061420.25972696X-RAY DIFFRACTION96.33
1.67-1.710.26231410.22862674X-RAY DIFFRACTION96.37
1.71-1.760.28671410.23132684X-RAY DIFFRACTION96.81
1.76-1.810.22221420.22712692X-RAY DIFFRACTION96.46
1.81-1.870.27251350.22672572X-RAY DIFFRACTION91.92
1.87-1.940.25051440.20952727X-RAY DIFFRACTION97.29
1.94-2.020.2281420.19912707X-RAY DIFFRACTION97.54
2.02-2.110.22191430.19912711X-RAY DIFFRACTION97.37
2.11-2.220.25731430.19072714X-RAY DIFFRACTION97.34
2.22-2.360.21221430.20442716X-RAY DIFFRACTION96.65
2.36-2.540.2271410.19762691X-RAY DIFFRACTION95.87
2.54-2.790.22641460.20412758X-RAY DIFFRACTION98.11
2.79-3.20.18921440.19122737X-RAY DIFFRACTION97.4
3.2-4.030.20431420.16652700X-RAY DIFFRACTION96.05
4.03-43.730.16741470.17062808X-RAY DIFFRACTION97.4
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)
10.006351662906720.0004269786751790.00341508041330.001108074514980.0001566974998820.001544940615770.01000093881120.02169794245340.0189635097964-0.0193199829649-0.0895001571242-0.0467081737193-0.0882656001766-0.0103107808445-2.36881025419E-50.2594379508150.09865290626010.03459075612610.2479465820510.03188096316920.2742250750984.9491451463714.935370123818.278825931
20.006982731266910.0094704940033-0.001986286603560.0373866928644-0.01706647564410.00909549584811-0.0006152330523770.007927182206050.00665749661577-0.0065659202591-0.02947435091540.0144036138215-0.0405192070638-0.0401461490221-0.007838835561690.2170256194320.1256858351610.0249906575780.282012134825-0.0206952878240.306844925314-3.5550471339112.480900971220.8773182981
30.008159794715330.003825910168070.002374853167860.00430993922481-0.001616789424890.00591186413330.020426492322-0.00776774281273-0.001453701047640.03165756913570.01753183236910.03759716660560.0038790119733-0.03491901876240.004050257651150.2087203224640.05424814501620.07238246869440.241980568333-0.02026214188050.305567658625-0.5015543216215.9440805650533.1683880079
40.005231144575670.0002291697194160.004703982816960.00316342316453-0.00390693468110.004728922955320.1469272902570.0609523166232-0.0339897481475-0.0370066976608-0.04740574402960.06058639226620.00739975728316-0.0453932640996-6.33098996129E-50.2492645420260.0859506993086-0.04603096139870.25779222826-0.04453252185370.2827955411361.203422844450.97811923405617.232028534
50.0704091458278-0.00744960461720.01640466994690.0571201768211-0.01294561820320.09790039058880.06005636306130.157684005205-0.089773503106-0.0991730453769-0.06029187082850.009178656235340.1069473872970.052254140780.00798859104860.3454134384730.3296667862170.02753815935890.414891782725-0.04813250154920.1987553968215.332668176-0.7780768319578.65249566109
60.0498363091841-0.0901713068041-0.007007493393870.172480264777-0.01275373232820.05470954282310.1058989829080.1302386491690.0133984299556-0.02406285251350.0394166318121-0.05738121290670.02763364170740.02443406330460.245019024420.2802151599340.3993459863420.002455758329120.457595569969-0.04737128082330.24258204453323.3076798615-6.7765018414.3743233309
70.0205969690520.00909041327434-0.01445497928180.08304228902270.02032895192690.01985701374410.0245963272010.0523143305646-0.0254951975767-0.100181966672-0.04117671368920.03746924875620.05012502567460.053628861006-0.01807383291610.4810648124220.366199531625-0.02956109238650.52452419438-0.07766388898410.1872536034218.772291394770.5331351064433.62285789356
80.1565342274090.0280249357350.0690743870340.007647758639380.02724845971740.08584971766330.1468950628830.1810203649620.0102389333157-0.047707619941-0.00246255141213-0.117427901527-0.00180611614786-0.01040410252910.2463332832130.2450976489970.2553704104840.02797989509970.4427778190420.02827263248340.24362087700525.6402847236-2.5584595630218.1939866762
90.164665524730.2706186804030.06660467368850.5279194428370.1129854361390.02755515492570.1693795657220.1007194997310.08993232439110.0877531413883-0.182563693312-0.02299934513520.02776977319490.08035067922220.01382296462310.1985389120740.09372269243350.0240973792610.2876671618130.03406926900650.23177034466512.20776035348.2833165196821.7817894677
100.0344188575520.0297117711344-0.0131055677620.0241819889818-0.01063340459930.005765779138760.1555485750550.0550888659117-0.199178742352-0.0294626679068-0.1156142401610.1771781137230.09421287135060.022554034896-0.00253941852470.3323426955510.106659086543-0.1090244908520.246356804981-0.07042316503930.2860582282434.06527453192-7.1266099425920.6863687274
110.001469953611780.00231783424476-0.004348424513610.00210082014038-0.003671288720350.00455413185770.0409046908028-0.0175097150894-0.06458999979380.024776212832-0.0247283238652-0.01741632883120.07293795465450.06552748318355.92901353573E-60.3040187836570.0424586289525-0.06148207695970.1757289282840.01533464082660.27370127861618.6736077166-10.373965722235.9927606088
120.00183201960432-0.00179072682080.0033905983250.0104568421742-0.009902632365130.007155430303870.09315476228-0.00962731537194-0.163632282629-0.04955328612120.003914616701040.06415651966050.1298074434290.018861836995-3.62780146106E-50.294866628430.0368070580786-0.05742602283350.166353368799-0.00561722360520.2978502082325.84819040809-9.3725033843629.7336971183
130.08581017205950.07792623366490.0105215955570.0857907204183-0.0008239545493650.06069744602090.1699005328970.0572113482081-0.07987313758270.0252411307944-0.09091653373240.09700151754110.1328234958850.03280349472960.1249329879860.2287766345150.0901337813476-0.0128550970340.167819222164-0.02342654573850.24233552071410.4637527914-1.1153269194126.8909652626
140.0006768087823740.00164893756555-0.0004392325679340.002027842368030.001469963139590.003432610233360.01608662403940.03843645267860.04882749008010.00188858797705-0.0336892818926-0.0409489998689-0.01208830139280.0297063900182-0.00197548530820.1675500908240.06050659458040.05404450642130.3017533502370.07287443140920.37056599296926.5043323898.8714254162322.7875986895
150.0138599375179-0.0102822989272-0.01524943624130.008102133881460.01184657074670.01689293359320.02659426804370.0349440718043-0.0034478471356-0.003181737877780.00425020227143-0.009322631329740.0148356497507-0.009444339084530.01343156581920.6697305343870.3705473543533.92328943759E-50.733076398824-0.1081934859370.30153224020111.7090081131-1.31278926303-2.8278478229
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1C through 7 )
2X-RAY DIFFRACTION2chain 'L' and (resid 8 through 14B)
3X-RAY DIFFRACTION3chain 'L' and (resid 14C through 14K)
4X-RAY DIFFRACTION4chain 'H' and (resid 16 through 29 )
5X-RAY DIFFRACTION5chain 'H' and (resid 30 through 50 )
6X-RAY DIFFRACTION6chain 'H' and (resid 51 through 60I)
7X-RAY DIFFRACTION7chain 'H' and (resid 61 through 80 )
8X-RAY DIFFRACTION8chain 'H' and (resid 81 through 103 )
9X-RAY DIFFRACTION9chain 'H' and (resid 104 through 140 )
10X-RAY DIFFRACTION10chain 'H' and (resid 141 through 164 )
11X-RAY DIFFRACTION11chain 'H' and (resid 165 through 179 )
12X-RAY DIFFRACTION12chain 'H' and (resid 180 through 193 )
13X-RAY DIFFRACTION13chain 'H' and (resid 194 through 231 )
14X-RAY DIFFRACTION14chain 'H' and (resid 232 through 246 )
15X-RAY DIFFRACTION15chain 'I' and (resid 517 through 527 )

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