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Yorodumi- PDB-9czd: Crystal structure of integrin avb6 headpiece in complex with comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9czd | ||||||
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Title | Crystal structure of integrin avb6 headpiece in complex with compound 30 | ||||||
Components |
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Keywords | CELL ADHESION/IMMUNE SYSTEM / avb6 integrin / fibrosis / idiopathic pulmonary fibrosis / free energy perturbation / CELL ADHESION / CELL ADHESION-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / enamel mineralization ...Langerhans cell differentiation / integrin alphav-beta8 complex / integrin alphav-beta6 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / enamel mineralization / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / bronchiole development / Laminin interactions / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / alphav-beta3 integrin-HMGB1 complex / phospholipid homeostasis / negative regulation of lipid transport / regulation of phagocytosis / negative regulation of low-density lipoprotein receptor activity / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / surfactant homeostasis / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / positive regulation of intracellular signal transduction / cell adhesion mediated by integrin / microvillus membrane / negative chemotaxis / Syndecan interactions / skin development / lung alveolus development / cell-substrate adhesion / endodermal cell differentiation / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / fibronectin binding / negative regulation of lipid storage / ECM proteoglycans / vasculogenesis / Integrin cell surface interactions / voltage-gated calcium channel activity / specific granule membrane / coreceptor activity / phagocytic vesicle / extrinsic apoptotic signaling pathway in absence of ligand / ERK1 and ERK2 cascade / positive regulation of cell adhesion / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / Signal transduction by L1 / molecular function activator activity / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / cellular response to ionizing radiation / protein kinase C binding / calcium ion transmembrane transport / wound healing / bone development / response to virus / cell morphogenesis / VEGFA-VEGFR2 Pathway / cell-cell adhesion / ruffle membrane / integrin binding / cell migration / cell junction / virus receptor activity / positive regulation of cytosolic calcium ion concentration / protease binding / angiogenesis / receptor complex / cell adhesion / positive regulation of cell migration / inflammatory response / immune response / symbiont entry into host cell / external side of plasma membrane / focal adhesion / centrosome / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular exosome / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | ||||||
Authors | Monroy, M.F. / Qiao, Q. / Lin, F.Y. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: The Discovery of MORF-627, a Highly Selective Conformationally-Biased Zwitterionic Integrin alpha v beta 6 Inhibitor for Fibrosis. Authors: Harrison, B.A. / Dowling, J.E. / Bursavich, M.G. / Troast, D.M. / Chong, K.M. / Hahn, K.N. / Zhong, C. / Mulvihill, K.M. / Nguyen, H. / Monroy, M.F. / Qiao, Q. / Sosa, B. / Mostafavi, S. / ...Authors: Harrison, B.A. / Dowling, J.E. / Bursavich, M.G. / Troast, D.M. / Chong, K.M. / Hahn, K.N. / Zhong, C. / Mulvihill, K.M. / Nguyen, H. / Monroy, M.F. / Qiao, Q. / Sosa, B. / Mostafavi, S. / Smukste, I. / Lee, D. / Cappellucci, L. / Konopka, E.H. / Nowakowski, P. / Stawski, L. / Senices, M. / Nguyen, M.H. / Kapoor, P.S. / Luus, L. / Sullivan, A. / Bortolato, A. / Svensson, M. / Hickey, E.R. / Konze, K.D. / Day, T. / Kim, B. / Negri, A. / Gerasyuto, A.I. / Moy, T.I. / Lu, M. / Ray, A.S. / Wang, L. / Cui, D. / Lin, F.Y. / Lippa, B. / Rogers, B.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9czd.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb9czd.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9czd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9czd_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 9czd_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 9czd_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 9czd_validation.cif.gz | 78.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cz/9czd ftp://data.pdbj.org/pub/pdb/validation_reports/cz/9czd | HTTPS FTP |
-Related structure data
Related structure data | 9cz7C 9czaC 9czfC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 66456.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAV, MSK8, VNRA, VTNR / Production host: Homo sapiens (human) / References: UniProt: P06756 |
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#2: Protein | Mass: 52714.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB6 / Production host: Homo sapiens (human) / References: UniProt: P18564 |
-Antibody , 2 types, 2 molecules CD
#3: Antibody | Mass: 23722.037 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
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#4: Antibody | Mass: 23209.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) |
-Sugars , 5 types, 6 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #13: Sugar | ChemComp-NAG / | |
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-Non-polymers , 6 types, 84 molecules
#9: Chemical | ChemComp-CA / #10: Chemical | ChemComp-GOL / #11: Chemical | ChemComp-A1A6H / ( | Mass: 511.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H38FN3O4 / Feature type: SUBJECT OF INVESTIGATION #12: Chemical | ChemComp-MG / | #14: Chemical | #15: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 13% PEG 3350, 100 mM HEPES pH 7.1, 200 mM ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97673 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97673 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→57.07 Å / Num. obs: 105035 / % possible obs: 99.86 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 12.54 |
Reflection shell | Resolution: 2.23→2.31 Å / Num. unique obs: 7670 / CC1/2: 0.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→57.07 Å / SU ML: 0.3162 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.2164 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.23→57.07 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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