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- PDB-1ycp: THE CRYSTAL STRUCTURE OF FIBRINOGEN-AA PEPTIDE 1-23 (F8Y) BOUND T... -
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Basic information
Entry | Database: PDB / ID: 1ycp | ||||||
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Title | THE CRYSTAL STRUCTURE OF FIBRINOGEN-AA PEPTIDE 1-23 (F8Y) BOUND TO BOVINE THROMBIN EXPLAINS WHY THE MUTATION OF PHE-8 TO TYROSINE STRONGLY INHIBITS NORMAL CLEAVAGE AT ARGININE-16 | ||||||
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![]() | HYDROLASE/HYDROLASE SUBSTRATE / FIBRINOPEPTIDE-A / COMPLEX (SERINE PROTEASE-PEPTIDE) / THROMBIN / HYDROLASE-HYDROLASE SUBSTRATE COMPLEX | ||||||
Function / homology | ![]() blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) ...blood coagulation, common pathway / induction of bacterial agglutination / fibrinogen complex / Regulation of TLR by endogenous ligand / fibrinogen binding / platelet alpha granule / blood coagulation, fibrin clot formation / MyD88 deficiency (TLR2/4) / positive regulation of heterotypic cell-cell adhesion / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / thrombin / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein polymerization / Integrin cell surface interactions / positive regulation of blood coagulation / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of vasoconstriction / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / acute-phase response / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / platelet aggregation / response to calcium ion / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / innate immune response / signaling receptor binding / calcium ion binding / structural molecule activity / cell surface / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Malkowski, M.G. / Edwards, B.F.P. | ||||||
![]() | ![]() Title: Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16. Authors: Malkowski, M.G. / Martin, P.D. / Lord, S.T. / Edwards, B.F. #1: ![]() Title: Bovine Thrombin Complexed with an Uncleavable Analog of Residues 7-19 of Fibrinogen a Alpha: Geometry of the Catalytic Triad and Interactions of the P1', P2', and P3' Substrate Residues Authors: Martin, P.D. / Malkowski, M.G. / Dimaio, J. / Konishi, Y. / Ni, F. / Edwards, B.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130.5 KB | Display | ![]() |
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PDB format | ![]() | 105.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.5 KB | Display | ![]() |
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Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | THERE ARE TWO INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT: COMPLEX 1 EPSILON THROMBIN: CHAINS J, K, M FIBRINOPEPTIDE: CHAIN F COMPLEX 2 ALPHA THROMBIN: CHAINS L, H FIBRINOPEPTIDE: CHAIN N |
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Components
-Protein/peptide , 2 types, 4 molecules LJFN
#1: Protein/peptide | Mass: 5735.240 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein/peptide | Mass: 2349.497 Da / Num. of mol.: 2 / Fragment: RESIDUES 1 - 23 / Mutation: F308Y Source method: isolated from a genetically manipulated source References: UniProt: P02671 |
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-Protein , 3 types, 3 molecules HKM
#2: Protein | Mass: 29772.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#4: Protein | Mass: 17525.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#5: Protein | Mass: 12265.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 1 types, 276 molecules ![](data/chem/img/HOH.gif)
#6: Water | ChemComp-HOH / |
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-Details
Sequence details | CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ...CHYMOTRYPS |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.26 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 2.0M AMMONIUM SULFATE 0.1M HEPES, PH 7.5 2.0% POLYETHYLENE GLYCOL 400 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→7 Å / Num. obs: 18614 / % possible obs: 63 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.109 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 25 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(I): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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