[English] 日本語
Yorodumi- PDB-1fzf: CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH THE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fzf | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH THE PEPTIDE LIGAND GLY-HIS-ARG-PRO-AMIDE | ||||||
Components | (FIBRINOGEN) x 4 | ||||||
Keywords | BLOOD COAGULATION / PLASMA / PLATELET / FIBRINOGEN / FIBRIN | ||||||
Function / homology | Function and homology information platelet maturation / 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 / cellular response to interleukin-6 / MyD88 deficiency (TLR2/4) ...platelet maturation / 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 / cellular response to interleukin-6 / 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 secretion / 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 / cell adhesion molecule binding / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK 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 / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / 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 / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Everse, S.J. / Spraggon, G. / Veerapandian, L. / Doolittle, R.F. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide. Authors: Everse, S.J. / Spraggon, G. / Veerapandian, L. / Doolittle, R.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fzf.cif.gz | 267.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fzf.ent.gz | 219.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fzf_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1fzf_full_validation.pdf.gz | 472.2 KB | Display | |
Data in XML | 1fzf_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 1fzf_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/1fzf ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fzf | HTTPS FTP |
-Related structure data
Related structure data | 1fzeC 1fzgC 1fzcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.24, 0.965, 0.104), Vector: |
-Components
-Protein , 3 types, 6 molecules ADBECF
#1: Protein | Mass: 10244.963 Da / Num. of mol.: 2 / Fragment: FRAGMENT DOUBLE-D / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P02671 #2: Protein | Mass: 37691.992 Da / Num. of mol.: 2 / Fragment: FRAGMENT DOUBLE-D / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P02675 #3: Protein | Mass: 36223.281 Da / Num. of mol.: 2 / Fragment: FRAGMENT DOUBLE-D / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P02679 |
---|
-Protein/peptide / Sugars / Non-polymers , 3 types, 12 molecules STMN
#4: Protein/peptide | Mass: 467.522 Da / Num. of mol.: 4 / Fragment: FRAGMENT DOUBLE-D / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P02675 #5: Sugar | #6: Chemical | ChemComp-CA / |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.8 / Details: pH 7.8 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 297 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. obs: 49458 / % possible obs: 88.5 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.119 |
Reflection | *PLUS Num. measured all: 232395 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FZC Resolution: 2.7→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |