[English] 日本語
Yorodumi
- PDB-4ueh: Thrombin in complex with benzamidine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ueh
TitleThrombin in complex with benzamidine
Components
  • HIRUDIN VARIANT-2
  • THROMBIN HEAVY CHAIN
  • THROMBIN LIGHT CHAIN
KeywordsHYDROLASE / HYDROLASE INHIBITOR COMPLEX / SERINE PROTEASE / BLOOD COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / BLOOD CLOTTING INHIBITOR / THROMBIN INHIBITOR / FRAGMENT / GLYCOSYLATION / BLOOD
Function / homology
Function and homology information


positive regulation of lipid kinase activity / 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 / 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 / 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 / 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 / Regulation of Complement cascade / acute-phase response / 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 / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / 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
Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain ...Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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
BENZAMIDINE / PHOSPHATE ION / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HIRUDO MEDICINALIS (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å
AuthorsRuehmann, E. / Heine, A. / Klebe, G.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Fragments Can Bind Either More Enthalpy or Entropy-Driven: Crystal Structures and Residual Hydration Pattern Suggest Why.
Authors: Ruehmann, E. / Betz, M. / Heine, A. / Klebe, G.
History
DepositionDec 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_struct_special_symmetry / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: THROMBIN HEAVY CHAIN
I: HIRUDIN VARIANT-2
L: THROMBIN LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2079
Polymers34,6333
Non-polymers5746
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-32.6 kcal/mol
Surface area12700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.421, 71.512, 72.465
Angle α, β, γ (deg.)90.00, 100.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-75-

ARG

-
Components

-
Protein/peptide , 2 types, 2 molecules IL

#2: Protein/peptide HIRUDIN VARIANT-2


Mass: 1548.580 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 61-72 / Source method: obtained synthetically / Details: HIRUDIN (54-65) (SULFATED) / Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P09945
#3: Protein/peptide THROMBIN LIGHT CHAIN / PROTHROMBIN / COAGULATION FACTOR II / ACTIVATION PEPTIDE FRAGMENT 1 / ACTIVATION PEPTIDE FRAGMENT 2 ...PROTHROMBIN / COAGULATION FACTOR II / ACTIVATION PEPTIDE FRAGMENT 1 / ACTIVATION PEPTIDE FRAGMENT 2 / ALPHA THROMBIN


Mass: 3432.829 Da / Num. of mol.: 1 / Fragment: THROMBIN LIGHT CHAIN, UNP RESIDUES 333-361 / Source method: isolated from a natural source / Details: PURIFIED FROM HUMAN BLOOD PLASMA / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00734, thrombin

-
Protein / Sugars , 2 types, 2 molecules H

#1: Protein THROMBIN HEAVY CHAIN / PROTHROMBIN / COAGULATION FACTOR II / ACTIVATION PEPTIDE FRAGMENT 1 / ACTIVATION PEPTIDE FRAGMENT 2 ...PROTHROMBIN / COAGULATION FACTOR II / ACTIVATION PEPTIDE FRAGMENT 1 / ACTIVATION PEPTIDE FRAGMENT 2 / ALPHA THROMBIN


Mass: 29651.105 Da / Num. of mol.: 1 / Fragment: THROMBIN HEAVY CHAIN, UNP RESIDUES 364-621 / Source method: isolated from a natural source / Details: PURIFIED FROM HUMAN BLOOD PLASMA / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P00734, thrombin
#4: 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: 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

-
Non-polymers , 5 types, 342 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsGLU 1C WAS NOT BUILD DUE TO LACK OF ELECTRON DENSITY RESIDUES 148-149E WERE NOT BUILD DUE TO LACK ...GLU 1C WAS NOT BUILD DUE TO LACK OF ELECTRON DENSITY RESIDUES 148-149E WERE NOT BUILD DUE TO LACK OF ELECTRON DENSITY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.57 % / Description: NONE
Crystal growpH: 7.5
Details: SEE MATERIALS AND METHODS SECTION OF PUBLICATION, pH 7.5

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.16→35.76 Å / Num. obs: 444822 / % possible obs: 95.7 % / Observed criterion σ(I): 2.5 / Redundancy: 3.8 % / Biso Wilson estimate: 13.55 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.7
Reflection shellResolution: 1.16→1.2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.52 / % possible all: 84.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8D

1h8d


Resolution: 1.16→35.756 Å / SU ML: 0.09 / σ(F): 1.37 / Phase error: 11.98 / Stereochemistry target values: ML
Details: RESIDUES 148-149E ARE DISORDERED. DISORDERED REGIONS WERE NOT MODELED.
RfactorNum. reflection% reflection
Rfree0.1383 5835 5 %
Rwork0.1207 --
obs0.1216 116707 95.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22 Å2
Refinement stepCycle: LAST / Resolution: 1.16→35.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 36 337 2692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112547
X-RAY DIFFRACTIONf_angle_d1.4583470
X-RAY DIFFRACTIONf_dihedral_angle_d14.9471017
X-RAY DIFFRACTIONf_chiral_restr0.089367
X-RAY DIFFRACTIONf_plane_restr0.009449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1599-1.17310.23061520.23522885X-RAY DIFFRACTION74
1.1731-1.18690.20861730.20623284X-RAY DIFFRACTION86
1.1869-1.20130.20771860.17833549X-RAY DIFFRACTION93
1.2013-1.21650.17081930.16533651X-RAY DIFFRACTION94
1.2165-1.23260.19431920.15863655X-RAY DIFFRACTION95
1.2326-1.24940.15881930.14383657X-RAY DIFFRACTION95
1.2494-1.26730.15471910.14013645X-RAY DIFFRACTION95
1.2673-1.28620.16711950.13763701X-RAY DIFFRACTION95
1.2862-1.30630.16251920.12773638X-RAY DIFFRACTION95
1.3063-1.32770.14391950.11873707X-RAY DIFFRACTION96
1.3277-1.35060.14371940.10883691X-RAY DIFFRACTION96
1.3506-1.37520.13211950.10553697X-RAY DIFFRACTION96
1.3752-1.40160.13641950.1033712X-RAY DIFFRACTION96
1.4016-1.43020.12671970.09563736X-RAY DIFFRACTION96
1.4302-1.46130.11491930.09453684X-RAY DIFFRACTION97
1.4613-1.49530.10771960.08523712X-RAY DIFFRACTION97
1.4953-1.53270.10811980.0853756X-RAY DIFFRACTION97
1.5327-1.57420.11491970.07963760X-RAY DIFFRACTION97
1.5742-1.62050.11091980.08163763X-RAY DIFFRACTION98
1.6205-1.67280.10361980.08043753X-RAY DIFFRACTION98
1.6728-1.73260.10681980.08213765X-RAY DIFFRACTION97
1.7326-1.8020.10541980.08623755X-RAY DIFFRACTION98
1.802-1.8840.12662000.09583800X-RAY DIFFRACTION98
1.884-1.98330.12361990.10043788X-RAY DIFFRACTION98
1.9833-2.10750.11822010.10613818X-RAY DIFFRACTION99
2.1075-2.27020.13612020.10843841X-RAY DIFFRACTION99
2.2702-2.49860.14222020.11953831X-RAY DIFFRACTION99
2.4986-2.86010.14972010.13223828X-RAY DIFFRACTION99
2.8601-3.60280.13942050.14193892X-RAY DIFFRACTION99
3.6028-35.7730.15692060.14553918X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more