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- PDB-1eb1: Complex structure of human thrombin with N-methyl-arginine inhibitor -

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Basic information

Entry
Database: PDB / ID: 1eb1
TitleComplex structure of human thrombin with N-methyl-arginine inhibitor
Components
  • 3-CYCLOHEXYL-D-ALANYL-L-PROLYL-N~2~-METHYL-L-ARGININE
  • PEPTIDE INHIBITOR
  • THROMBIN HEAVY CHAIN
  • THROMBIN LIGHT CHAIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEINASE / BLOOD COAGULATION / CALCIUM-BINDING / GLYCOPROTEIN / KRINGLE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / 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 / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / 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 / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / 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
3-cyclohexyl-D-alanyl-L-prolyl-N~2~-methyl-L-arginine / Prothrombin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFriedrich, R. / Steinmetzer, T. / Bode, W.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: The Methyl Group of N(Alpha)(Me)Arg-Containing Peptides Disturbs the Active-Site Geometry of Thrombin, Impairing Efficient Cleavage
Authors: Friedrich, R. / Steinmetzer, T. / Huber, R. / Sturzebecher, J. / Bode, W.
History
DepositionJul 18, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2002Provider: 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 21, 2012Group: Data collection / Database references / Other
Revision 1.3Nov 30, 2012Group: Other
Revision 1.4Feb 8, 2017Group: Source and taxonomy / Structure summary
Revision 1.5Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Revision 1.6Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HB" 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
A: PEPTIDE INHIBITOR
H: THROMBIN HEAVY CHAIN
L: THROMBIN LIGHT CHAIN
B: 3-CYCLOHEXYL-D-ALANYL-L-PROLYL-N~2~-METHYL-L-ARGININE


Theoretical massNumber of molelcules
Total (without water)34,4314
Polymers34,4314
Non-polymers00
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.839, 71.508, 71.710
Angle α, β, γ (deg.)90.00, 99.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-2030-

HOH

21H-2099-

HOH

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Components

#1: Protein/peptide PEPTIDE INHIBITOR


Mass: 1209.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Protein THROMBIN HEAVY CHAIN


Mass: 29594.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: BLOOD / References: UniProt: P00734
#3: Protein/peptide THROMBIN LIGHT CHAIN


Mass: 3188.627 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN RESIDUES 364-620 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Organ: BLOOD / References: UniProt: P00734, thrombin
#4: Protein/peptide 3-CYCLOHEXYL-D-ALANYL-L-PROLYL-N~2~-METHYL-L-ARGININE


Type: Peptide-like / Class: Thrombin inhibitor / Mass: 438.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
References: 3-cyclohexyl-D-alanyl-L-prolyl-N~2~-methyl-L-arginine
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBASED ON THE PRIMARY PUBLICATION J MOL BIOL. 2002 MAR 1;316(4):869- 74, THE LIGAND E1A WAS THE N- ...BASED ON THE PRIMARY PUBLICATION J MOL BIOL. 2002 MAR 1;316(4):869- 74, THE LIGAND E1A WAS THE N-TERMINAL FRAGMENT CLEAVED FROM THE DESIGNED BIVALENT PEPTIDIC THROMBIN INHIBITOR. THE C-TERMINAL FRAGMENT OF THIS INHIBITOR IS REPRESENTED BY CHAIN A, E1A IS BUILT WITH TERMINAL OXT THAT IS NOT OBSERVED, CONSIDERING THE NATURE OF PEPTIDASE CLEAVAGE.

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 8 / Details: PH 8.00
Crystal grow
*PLUS
Method: other / Details: Steinmetzer, T., (2000) Biol. Chem., 381, 603.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→17 Å / Num. obs: 30387 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.5 / % possible all: 92.6
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 17 Å / Redundancy: 2.2 % / Num. measured all: 156090
Reflection shell
*PLUS
% possible obs: 92.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HGT

2hgt


Resolution: 1.8→16.74 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1230607.77 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1206 4 %SHELLS
Rwork0.191 ---
obs0.191 30147 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å20 Å2-2.93 Å2
2---2.51 Å20 Å2
3----1.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-20 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→16.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2419 0 0 320 2739
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 179 3.7 %
Rwork0.263 4703 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TRI.PARTRI.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 17 Å / Num. reflection obs: 29169 / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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