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- PDB-6t56: Thrombin in Complex with Benzylamine -

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Basic information

Entry
Database: PDB / ID: 6t56
TitleThrombin in Complex with Benzylamine
Components
  • (ProthrombinThrombin) x 2
  • Hirudin variant-2
KeywordsHYDROLASE / COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / SERINE PROTEASE / PROTEASE
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 / negative regulation of cytokine production involved in inflammatory response / positive regulation of collagen biosynthetic process / 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 / regulation of cytosolic calcium ion concentration / fibrinolysis / 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
BENZYLAMINE / PHOSPHATE ION / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsNgo, K. / Abazi, N. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: Thrombin in Complex with Benzylamine
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,03710
Polymers35,3683
Non-polymers6697
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-26 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.553, 71.037, 72.806
Angle α, β, γ (deg.)90.000, 100.482, 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-75-

ARG

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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
#8: 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 , 5 types, 228 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ABN / BENZYLAMINE / Benzylamine


Mass: 107.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9N / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
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: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.31→43.528 Å / Num. obs: 82966 / % possible obs: 97.8 % / Redundancy: 3.06 % / Biso Wilson estimate: 14.96 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.052 / Rsym value: 0.043 / Net I/σ(I): 12.63
Reflection shellResolution: 1.31→1.91 Å / Mean I/σ(I) obs: 2.08 / Num. unique obs: 13286 / CC1/2: 0.772 / Rsym value: 0.521

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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: 1.31→34.69 Å / SU ML: 0.1207 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.8298
RfactorNum. reflection% reflection
Rfree0.1632 4148 5 %
Rwork0.1403 --
obs0.1415 82956 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.52 Å2
Refinement stepCycle: LAST / Resolution: 1.31→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 43 222 2585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692509
X-RAY DIFFRACTIONf_angle_d0.99873399
X-RAY DIFFRACTIONf_chiral_restr0.0857351
X-RAY DIFFRACTIONf_plane_restr0.0069454
X-RAY DIFFRACTIONf_dihedral_angle_d19.0743969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.320.25951330.25072526X-RAY DIFFRACTION94.73
1.32-1.340.28031380.23412621X-RAY DIFFRACTION97.59
1.34-1.360.27571410.22172665X-RAY DIFFRACTION98.35
1.36-1.370.26131340.20432559X-RAY DIFFRACTION97.57
1.37-1.390.23161390.19192625X-RAY DIFFRACTION97.63
1.39-1.410.24571360.19242601X-RAY DIFFRACTION97.58
1.41-1.430.23321390.18682637X-RAY DIFFRACTION97.3
1.43-1.450.20911360.17012583X-RAY DIFFRACTION97.39
1.45-1.480.18851400.15782653X-RAY DIFFRACTION98.9
1.48-1.50.18471360.14772589X-RAY DIFFRACTION98.73
1.5-1.530.1821410.13862672X-RAY DIFFRACTION98.39
1.53-1.550.17021370.1252618X-RAY DIFFRACTION98.53
1.55-1.580.15711390.11732635X-RAY DIFFRACTION98.44
1.58-1.620.14281400.12122660X-RAY DIFFRACTION98.11
1.62-1.650.13861360.11122583X-RAY DIFFRACTION97.77
1.65-1.690.13941360.11252591X-RAY DIFFRACTION96.57
1.69-1.730.13381400.1122658X-RAY DIFFRACTION98.04
1.73-1.780.16541380.10792622X-RAY DIFFRACTION98.4
1.78-1.830.12991380.1112621X-RAY DIFFRACTION98.75
1.83-1.890.13751400.1152654X-RAY DIFFRACTION99.15
1.89-1.960.14461410.1152675X-RAY DIFFRACTION99.09
1.96-2.030.14131400.11492664X-RAY DIFFRACTION98.98
2.03-2.130.14011370.12192603X-RAY DIFFRACTION96.68
2.13-2.240.13631370.12372609X-RAY DIFFRACTION97.48
2.24-2.380.14611420.132681X-RAY DIFFRACTION99.3
2.38-2.560.17321390.13422648X-RAY DIFFRACTION99.08
2.56-2.820.16971410.14712677X-RAY DIFFRACTION98.67
2.82-3.230.17781350.15552576X-RAY DIFFRACTION95.49
3.23-4.070.13741410.14442672X-RAY DIFFRACTION98.22
4.07-34.690.18681380.15662630X-RAY DIFFRACTION95.15

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