+Open data
-Basic information
Entry | Database: PDB / ID: 6q1u | ||||||
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Title | Structure of plasmin and peptide complex | ||||||
Components |
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Keywords | BLOOD CLOTTING / serine protease / cyclic peptide / complex / antifibrinolysis | ||||||
Function / homology | Function and homology information plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of endopeptidase activity ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of endopeptidase activity / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / endopeptidase inhibitor activity / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / Schaffer collateral - CA1 synapse / serine-type endopeptidase inhibitor activity / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Helianthus annuus (common sunflower) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3467 Å | ||||||
Authors | Wu, G. / Law, R.H.P. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Application and Structural Analysis of Triazole-Bridged Disulfide Mimetics in Cyclic Peptides. Authors: White, A.M. / de Veer, S.J. / Wu, G. / Harvey, P.J. / Yap, K. / King, G.J. / Swedberg, J.E. / Wang, C.K. / Law, R.H.P. / Durek, T. / Craik, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q1u.cif.gz | 233.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q1u.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 6q1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q1u_validation.pdf.gz | 1007.4 KB | Display | wwPDB validaton report |
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Full document | 6q1u_full_validation.pdf.gz | 1019.2 KB | Display | |
Data in XML | 6q1u_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 6q1u_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/6q1u ftp://data.pdbj.org/pub/pdb/validation_reports/q1/6q1u | HTTPS FTP |
-Related structure data
Related structure data | 6u22C 6u24C 6u7qC 6u7rC 6u7sC 6u7uC 6u7wC 6u7xC 6vxyC 6vy8C 6d3xS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27264.326 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P00747, plasmin #2: Protein/peptide | Mass: 1549.791 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: WHM is a triazole motif that replaces the disulphide bond Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM Sodium Citrate, 100 mM MgCl2, 18% PEG 4000 / PH range: 4-6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732013702 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953732013702 Å / Relative weight: 1 |
Reflection | Resolution: 2.3467→46.6908 Å / Num. obs: 22667 / % possible obs: 98.87 % / Redundancy: 4.2 % / Biso Wilson estimate: 21.72 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.097 / Rrim(I) all: 0.214 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.347→2.431 Å / Rmerge(I) obs: 0.714 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2197 / CC1/2: 0.819 / Rpim(I) all: 0.379 / Rrim(I) all: 0.814 / % possible all: 98.03 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6d3x Resolution: 2.3467→46.6908 Å / SU ML: 0.3543 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.6329
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3467→46.6908 Å
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Refine LS restraints |
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LS refinement shell |
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