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- PDB-2jh5: Human Thrombin Hirugen Inhibitor complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2jh5
TitleHuman Thrombin Hirugen Inhibitor complex
Components
  • HIRUDIN IIIA
  • THROMBIN HEAVY CHAIN
  • THROMBIN LIGHT CHAIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GLYCOPROTEIN / SERINE PROTEASE / KRINGLE / ZYMOGEN / THROMBIN / PROTEASE / DISEASE MUTATION / BLOOD COAGULATION / GAMMA-CARBOXYGLUTAMIC ACID / PROTEASE INHIBITOR / SERINE PROTEASE INHIBITOR / SULFATION / ACUTE PHASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-895 / Prothrombin / Hirudin-3A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HIRUDO MEDICINALIS (medicinal leech)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSenger, S. / Chan, C. / Convery, M.A. / Hubbard, J.A. / Young, R.J. / Shah, G.P. / Watson, N.S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Sulfonamide-Related Conformational Effects and Their Importance in Structure-Based Design.
Authors: Senger, S. / Chan, C. / Convery, M.A. / Hubbard, J.A. / Shah, G.P. / Watson, N.S. / Young, R.J.
History
DepositionFeb 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Mar 13, 2013Group: Other
Revision 1.4Aug 7, 2013Group: Derived calculations / Other
Revision 1.5Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: THROMBIN LIGHT CHAIN
D: THROMBIN HEAVY CHAIN
H: HIRUDIN IIIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7516
Polymers35,2403
Non-polymers5113
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-21.8 kcal/mol
Surface area15450 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.363, 71.478, 72.106
Angle α, β, γ (deg.)90.00, 100.62, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 2 types, 2 molecules CH

#1: Protein/peptide THROMBIN LIGHT CHAIN / / COAGULATION FACTOR II / ALPHA THROMBIN


Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 328-363 / Source method: isolated from a natural source / Details: LIGHT CHAIN HAS ONE DISULPHIDE BOND TO HEAVY CHAIN / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin
#3: Protein/peptide HIRUDIN IIIA / HIRUGEN


Mass: 1363.399 Da / Num. of mol.: 1 / Fragment: RESIDUES 55-64 / Source method: obtained synthetically / Details: RESIDUE 63 IS A SULFONATED TYROSINE / Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P28507

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Protein , 1 types, 1 molecules D

#2: Protein THROMBIN HEAVY CHAIN / / COAGULATION FACTOR II / ALPHA THROMBIN


Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 364-622 / Source method: isolated from a natural source / Details: LIGHT CHAIN HAS ONE DISULPHIDE BOND TO HEAVY CHAIN / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin

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Non-polymers , 4 types, 132 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-895 / 2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}ETHENESULFONAMIDE


Mass: 447.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22ClN3O5S2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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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: 51.21 %
Crystal growpH: 6.8 / Details: PH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: NONIUS / Detector: CCD / Date: May 20, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→19.71 Å / Num. obs: 11571 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 2.5→2.58 Å / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
REFMAC5.3.0006refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.71 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.244 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.599 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 581 4.8 %RANDOM
Rwork0.185 ---
obs0.188 11571 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.54 Å2
2---0.36 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 30 129 2505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222436
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9793292
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1115284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30423.504117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30915430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4241520
X-RAY DIFFRACTIONr_chiral_restr0.1050.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021850
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.21091
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21640
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2154
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.23821430
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44342305
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.98941059
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5276987
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.331 50
Rwork0.242 814

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