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- PDB-1dm4: SER195ALA MUTANT OF HUMAN THROMBIN COMPLEXED WITH FIBRINOPEPTIDE ... -

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Basic information

Entry
Database: PDB / ID: 1dm4
TitleSER195ALA MUTANT OF HUMAN THROMBIN COMPLEXED WITH FIBRINOPEPTIDE A (7-16)
Components
  • PROTEIN (ALPHA THROMBIN:LIGHT CHAIN)
  • PROTEIN (FIBRINOPEPTIDE)
  • PROTEIN (MUTANT ALPHA THROMBIN:HEAVY CHAIN)
KeywordsHYDROLASE / MUTANT THROMBIN / RESIDUAL CATALYTIC ACTIVITY / FIBRINOPEPTIDE A
Function / homology
Function and homology information


blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / extracellular matrix structural constituent / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / plasminogen activation / cytolysis by host of symbiont cells / p130Cas linkage to MAPK signaling for integrins / thrombospondin receptor activity / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / thrombin / positive regulation of peptide hormone secretion / negative regulation of astrocyte differentiation / positive regulation of vasoconstriction / 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) / GRB2:SOS provides linkage to MAPK signaling for Integrins / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / positive regulation of exocytosis / negative regulation of platelet activation / negative regulation of blood coagulation / protein polymerization / positive regulation of blood coagulation / negative regulation of fibrinolysis / Integrin cell surface interactions / 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 / negative regulation of endothelial cell apoptotic process / Removal of aminoterminal propeptides from gamma-carboxylated proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / Integrin signaling / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / platelet alpha granule lumen / Regulation of Complement cascade / cell-matrix adhesion / acute-phase response / positive regulation of protein secretion / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / Post-translational protein phosphorylation / lipopolysaccharide binding / growth factor activity / Signaling by high-kinase activity BRAF mutants / response to calcium ion / MAP2K and MAPK activation / positive regulation of insulin secretion / platelet activation / response to wounding / platelet aggregation / 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 / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / Signaling by BRAF and RAF1 fusions / Platelet degranulation / extracellular vesicle / ER-Phagosome pathway / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / protein-containing complex assembly / blood microparticle / protein-macromolecule adaptor activity / G alpha (q) signalling events / adaptive immune response / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Amyloid fiber formation / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity
Similarity search - Function
Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain ...Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal 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 / 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
Prothrombin / Fibrinogen alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsKrishnan, R. / Sadler, E.J. / Tulinsky, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of the Ser195Ala mutant of human alpha--thrombin complexed with fibrinopeptide A(7--16): evidence for residual catalytic activity.
Authors: Krishnan, R. / Sadler, J.E. / Tulinsky, A.
History
DepositionDec 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 7, 2011Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ALPHA THROMBIN:LIGHT CHAIN)
B: PROTEIN (MUTANT ALPHA THROMBIN:HEAVY CHAIN)
C: PROTEIN (FIBRINOPEPTIDE)


Theoretical massNumber of molelcules
Total (without water)34,9083
Polymers34,9083
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-21 kcal/mol
Surface area12260 Å2
MethodPISA
2
A: PROTEIN (ALPHA THROMBIN:LIGHT CHAIN)
B: PROTEIN (MUTANT ALPHA THROMBIN:HEAVY CHAIN)
C: PROTEIN (FIBRINOPEPTIDE)

A: PROTEIN (ALPHA THROMBIN:LIGHT CHAIN)
B: PROTEIN (MUTANT ALPHA THROMBIN:HEAVY CHAIN)
C: PROTEIN (FIBRINOPEPTIDE)


Theoretical massNumber of molelcules
Total (without water)69,8166
Polymers69,8166
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_755-x+2,-y+1/2,z1
Buried area9490 Å2
ΔGint-46 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.100, 135.100, 135.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein/peptide PROTEIN (ALPHA THROMBIN:LIGHT CHAIN)


Mass: 3939.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00734
#2: Protein PROTEIN (MUTANT ALPHA THROMBIN:HEAVY CHAIN)


Mass: 29921.414 Da / Num. of mol.: 1 / Mutation: S195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00734
#3: Protein/peptide PROTEIN (FIBRINOPEPTIDE)


Mass: 1047.144 Da / Num. of mol.: 1 / Fragment: FPA / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / References: UniProt: P02671*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.19 %
Crystal growpH: 7.5
Details: 1.4M SODIUM CITRATE, 1-2% ISOPROPANOL, 0.1M HEPES BUFFER, pH 7.50
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
21.4 Msodium citrate1reservoir
30.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Mar 7, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 9561 / % possible obs: 71 % / Observed criterion σ(I): 2 / Redundancy: 2.28 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 15
Reflection shellResolution: 2.5→2.75 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.19 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 15 Å / Observed criterion σ(I): 2 / Num. measured all: 21833
Reflection shell
*PLUS
% possible obs: 61 %

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Processing

Software
NameClassification
AMoREphasing
PROFFTrefinement
RefinementResolution: 2.5→7 Å / σ(F): 4 / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE. /
RfactorNum. reflection
all0.169 -
obs0.169 8330
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 0 149 2525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.042
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_planar_d0.057
X-RAY DIFFRACTIONp_chiral_restr0.18

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