[English] 日本語
Yorodumi- PDB-1n73: Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n73 | ||||||
---|---|---|---|---|---|---|---|
Title | Fibrin D-Dimer, Lamprey complexed with the PEPTIDE LIGAND: GLY-HIS-ARG-PRO-AMIDE | ||||||
Components |
| ||||||
Keywords | BLOOD CLOTTING / isopeptide cross-linked chains / protein-peptide complex | ||||||
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 / cellular response to leptin stimulus / 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 / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to leptin stimulus / 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 / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / protein polymerization / cellular response to interleukin-1 / Integrin cell surface interactions / 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 / positive regulation of protein secretion / 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 / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / cell cortex / ER-Phagosome pathway / protein-folding chaperone binding / protein-containing complex assembly / collagen-containing extracellular matrix / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / blood microparticle / external side of plasma membrane / innate immune response / signaling receptor binding / synapse / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Petromyzon marinus (sea lamprey) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Yang, Z. / Pandi, L. / Doolittle, R.F. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: The Crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface Authors: Yang, Z. / Pandi, L. / Doolittle, R.F. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE SEQUENCE MISMATCHES AT RESIDUE 153 OF CHAINS A,D: ALA CONFIRMED BY INDEPENDENT SEQUENCING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n73.cif.gz | 302 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n73.ent.gz | 245.9 KB | Display | PDB format |
PDBx/mmJSON format | 1n73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n73_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1n73_full_validation.pdf.gz | 542.8 KB | Display | |
Data in XML | 1n73_validation.xml.gz | 42.2 KB | Display | |
Data in CIF | 1n73_validation.cif.gz | 61 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/1n73 ftp://data.pdbj.org/pub/pdb/validation_reports/n7/1n73 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 14074.052 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Petromyzon marinus (sea lamprey) / Tissue: blood / References: UniProt: P02674 #2: Protein | Mass: 37061.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Petromyzon marinus (sea lamprey) / Tissue: blood / References: UniProt: P02678 #3: Protein | Mass: 38167.184 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Petromyzon marinus (sea lamprey) / Tissue: blood / References: UniProt: P04115 |
---|
-Protein/peptide / Sugars / Non-polymers , 3 types, 12 molecules GHIJ
#4: Protein/peptide | Mass: 467.522 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic peptide that occurs naturally in humans. / References: UniProt: P02675*PLUS #5: Sugar | ChemComp-NAG / #6: Chemical | ChemComp-CA / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.35 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 3350 Tris buffer 5 mM CaCl2 2 mM GHRPam, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 23, 2002 |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→20 Å / Num. all: 92116 / Num. obs: 75259 / % possible obs: 81.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.084 |
Reflection shell | Resolution: 2.9→3 Å / % possible all: 66.7 |
Reflection | *PLUS Num. obs: 40004 / Num. measured all: 75259 |
Reflection shell | *PLUS % possible obs: 66.7 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.308 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |