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Yorodumi- PDB-2m7h: The C-terminal Region of Disintegrin Modulate its 3D Conformation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2m7h | ||||||
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Title | The C-terminal Region of Disintegrin Modulate its 3D Conformation and Cooperate with RGD Loop in Regulating Integrin alpha-IIb beta-3 Recognition | ||||||
Components | Zinc metalloproteinase/disintegrin | ||||||
Keywords | HYDROLASE / Rhodostomin muant / RGD motif / C-terminal region mutations / integrin alpha-IIb beta-3 | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Calloselasma rhodostoma (Malayan pit viper) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | closest to the average, model8 | ||||||
Authors | Chuang, W. / Chang, Y. | ||||||
Citation | Journal: To be Published Title: The C-terminal Region of Disintegrin Modulate its 3D Conformation and Cooperate with RGD Loop in Regulating Recognitions of Integrins Authors: Chuang, W. / Chang, Y. / Shiu, J. / Chen, C. / Chen, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m7h.cif.gz | 386.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m7h.ent.gz | 334 KB | Display | PDB format |
PDBx/mmJSON format | 2m7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2m7h_validation.pdf.gz | 404.6 KB | Display | wwPDB validaton report |
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Full document | 2m7h_full_validation.pdf.gz | 573 KB | Display | |
Data in XML | 2m7h_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 2m7h_validation.cif.gz | 56.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/2m7h ftp://data.pdbj.org/pub/pdb/validation_reports/m7/2m7h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8759.756 Da / Num. of mol.: 1 / Fragment: UNP residues 408-478 / Mutation: P48A,M52W,P53N,Y67N,H68P,S69W,H70N,A71G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper) Gene: RHOD / Production host: Komagataella pastoris (fungus) References: UniProt: P30403, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 6 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 8 |