+Open data
-Basic information
Entry | Database: PDB / ID: 2ike | ||||||
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Title | Solution Structure of the second Clip domain in PAP2 | ||||||
Components | Prophenoloxidase activating proteinase-2 | ||||||
Keywords | HYDROLASE / BETA-SHEET / DOUBLE HELIX | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular space Similarity search - Function | ||||||
Biological species | Manduca sexta (tobacco hornworm) | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics | ||||||
Authors | Huang, R.D. / Lv, Z.Q. / Dai, H.E. / Velde, D.V. / Prakash, O. / Jiang, H.B. | ||||||
Citation | Journal: To be Published Title: Solution structure of Clip domain in PAP2 Authors: Huang, R.D. / Lv, Z.Q. / Dai, H.E. / Velde, D.V. / Prakash, O. / Jiang, H.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ike.cif.gz | 303.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ike.ent.gz | 262.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ike.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ike_validation.pdf.gz | 338.9 KB | Display | wwPDB validaton report |
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Full document | 2ike_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 2ike_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 2ike_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/2ike ftp://data.pdbj.org/pub/pdb/validation_reports/ik/2ike | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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: 5789.503 Da / Num. of mol.: 1 / Fragment: second Clip domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Gene: PAP-2 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q2FAY5, UniProt: Q8I917*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1 mM Dual-Clip domain U-15N,13C, 100 mM phosphate buffer NA, 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | pH: 8.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, molecular dynamics, matrix relaxation, torsion angle dynamics Software ordinal: 1 Details: the structures are based on a total of 753 restraints, 690 are NOE-derived distance constraints, 27 dihedral angle restraints, 36 distance restraints from hydrogen bonds | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |