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- PDB-3u8o: Human thrombin complexed with D-Phe-Pro-D-Arg-D-Thr -

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Basic information

Entry
Database: PDB / ID: 3u8o
TitleHuman thrombin complexed with D-Phe-Pro-D-Arg-D-Thr
Components
  • D-PHE-PRO-D-ARG-D-THR DERIVED DIRECT THROMBIN INHIBITOR
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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 / 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 / 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 / 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 / acute-phase response / Regulation of Complement cascade / 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 / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / 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
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. ...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
D-phenylalanyl-L-prolyl-N~5~-[amino(iminio)methyl]-D-ornithyl-D-threoninamide / IODIDE ION / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å
AuthorsFigueiredo, A.C. / Clement, C.C. / Philipp, M. / Pereira, P.J.B.
CitationJournal: Plos One / Year: 2012
Title: Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors.
Authors: Figueiredo, A.C. / Clement, C.C. / Zakia, S. / Gingold, J. / Philipp, M. / Pereira, P.J.
History
DepositionOct 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Other
Revision 1.2Jun 5, 2013Group: Other
Revision 1.3Jul 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_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_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_role / _struct_conn.pdbx_value_order / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Thrombin light chain
H: Thrombin heavy chain
I: D-PHE-PRO-D-ARG-D-THR DERIVED DIRECT THROMBIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4609
Polymers33,8173
Non-polymers6436
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-45 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.446, 72.680, 83.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 2 types, 2 molecules LI

#1: Protein/peptide Thrombin light chain / ALPHA-THROMBIN / Prothrombin


Mass: 3517.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide D-PHE-PRO-D-ARG-D-THR DERIVED DIRECT THROMBIN INHIBITOR


Type: Peptide-like / Class: Thrombin inhibitor / Mass: 518.609 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: synthetic DL peptide with sequence D-Phe-Pro-D-Arg-D-Thr
Source: (synth.) synthetic construct (others)
References: D-phenylalanyl-L-prolyl-N~5~-[amino(iminio)methyl]-D-ornithyl-D-threoninamide

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Protein / Sugars , 2 types, 2 molecules H

#2: Protein Thrombin heavy chain / ALPHA-THROMBIN / Prothrombin


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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, 449 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 50mM Tris, 50mM Bicine, 30mM NaF, 30mM NaBr, 30mM NaI, 11.5% MPD, 11.5% PEG-1000, 11.5% PEG-3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 14, 2009
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.28→47.252 Å / Num. obs: 87023 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rsym value: 0.048 / Net I/σ(I): 28.5
Reflection shellResolution: 1.28→1.35 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.183 / % possible all: 93.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.65 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.34 Å
Translation2.5 Å36.34 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASER2.1.4phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→36.34 Å / Occupancy max: 1 / Occupancy min: 0.02 / SU ML: 0.25 / σ(F): 1.36 / Phase error: 11.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.149 4377 5.04 %
Rwork0.128 --
obs0.129 86923 96.4 %
all-86923 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.76 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 18.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.0886 Å20 Å2-0 Å2
2--0.8391 Å20 Å2
3----0.9278 Å2
Refine analyzeLuzzati coordinate error obs: 0.122 Å
Refinement stepCycle: LAST / Resolution: 1.28→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2315 0 33 444 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132572
X-RAY DIFFRACTIONf_angle_d1.4773507
X-RAY DIFFRACTIONf_dihedral_angle_d13.4671028
X-RAY DIFFRACTIONf_chiral_restr0.1369
X-RAY DIFFRACTIONf_plane_restr0.01447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.29450.16171300.14782512X-RAY DIFFRACTION88
1.2945-1.30980.18051580.14862649X-RAY DIFFRACTION94
1.3098-1.32580.18081260.13552662X-RAY DIFFRACTION94
1.3258-1.34250.18191240.12672688X-RAY DIFFRACTION95
1.3425-1.36020.15141580.11442654X-RAY DIFFRACTION95
1.3602-1.37880.15011380.10952650X-RAY DIFFRACTION95
1.3788-1.39850.13971470.10332724X-RAY DIFFRACTION95
1.3985-1.41940.12791190.10412707X-RAY DIFFRACTION95
1.4194-1.44160.14041490.09792672X-RAY DIFFRACTION95
1.4416-1.46520.12051470.09822714X-RAY DIFFRACTION96
1.4652-1.49050.13351450.09662693X-RAY DIFFRACTION96
1.4905-1.51760.13881550.09742720X-RAY DIFFRACTION96
1.5176-1.54680.12651440.09472705X-RAY DIFFRACTION96
1.5468-1.57840.13431510.09362728X-RAY DIFFRACTION96
1.5784-1.61270.14741530.09272715X-RAY DIFFRACTION96
1.6127-1.65020.11281400.09352744X-RAY DIFFRACTION97
1.6502-1.69150.12181470.09632766X-RAY DIFFRACTION97
1.6915-1.73720.14831650.10262708X-RAY DIFFRACTION97
1.7372-1.78830.14261560.1122751X-RAY DIFFRACTION97
1.7883-1.8460.1631280.11392797X-RAY DIFFRACTION97
1.846-1.9120.12531490.11432794X-RAY DIFFRACTION98
1.912-1.98850.13811720.11442762X-RAY DIFFRACTION98
1.9885-2.0790.13161480.11562784X-RAY DIFFRACTION98
2.079-2.18860.13981520.1182812X-RAY DIFFRACTION98
2.1886-2.32570.13341510.11582817X-RAY DIFFRACTION98
2.3257-2.50530.17331330.1242872X-RAY DIFFRACTION98
2.5053-2.75730.14931380.13642861X-RAY DIFFRACTION99
2.7573-3.15610.17351330.15052912X-RAY DIFFRACTION99
3.1561-3.97560.14621400.14232923X-RAY DIFFRACTION99
3.9756-36.35460.17511810.17853050X-RAY DIFFRACTION99

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