+Open data
-Basic information
Entry | Database: PDB / ID: 1udk | ||||||
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Title | Solution Structure of Nawaprin | ||||||
Components | Nawaprin | ||||||
Keywords | UNKNOWN FUNCTION / antiparallel beta-sheet / spiral backbone configuration | ||||||
Function / homology | Function and homology information peptidase inhibitor activity / defense response to bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Naja nigricollis (spitting cobra) | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics | ||||||
Authors | Torres, A.M. / Wong, H.Y. / Desai, M. / Moochhala, S. / Kuchel, P.W. / Kini, R.M. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Identification of a Novel Family of Proteins in Snake Venoms: Purification and Structural Characterization of Nawaprin from Naja nigricollis Snake Venom Authors: Torres, A.M. / Wong, H.Y. / Desai, M. / Moochhala, S. / Kuchel, P.W. / Kini, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1udk.cif.gz | 278.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1udk.ent.gz | 232 KB | Display | PDB format |
PDBx/mmJSON format | 1udk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1udk_validation.pdf.gz | 339.2 KB | Display | wwPDB validaton report |
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Full document | 1udk_full_validation.pdf.gz | 452.6 KB | Display | |
Data in XML | 1udk_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 1udk_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1udk ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1udk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 5300.228 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja nigricollis (spitting cobra) / Secretion: venom / References: UniProt: P60589*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: 2D NOESY |
NMR details | Text: The structures were determined using standard 2D homonuclear techniques. |
-Sample preparation
Details | Contents: 1.7mM Nawaprin / Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: no salt added / pH: 3.1 / Pressure: ambient / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-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: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing, molecular dynamics, distance geometry, torsion angle dynamics Software ordinal: 1 Details: The structures are based on a total of 530 restraints, 503 are NOE-derived distance restraints, 9 dihedral angle restraints, 18 distance restraints from hydrogen bonds. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 3000 / Conformers submitted total number: 20 |