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Open data
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Basic information
Entry | Database: PDB / ID: 2k51 | ||||||
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Title | NMR Solution Structure of the Neurotrypsin Kringle Domain | ||||||
![]() | Neurotrypsin | ||||||
![]() | HYDROLASE / NEUROTRYPSIN / KRINGLE DOMAIN / DISULFIDE-RICH PROTEIN FOLD / SERINE ENDOPEPTIDASE / EXTRACELLULAR PROTEOLYSIS | ||||||
Function / homology | ![]() zymogen activation / exocytosis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / synaptic cleft / terminal bouton / peptidase activity / cytoplasmic vesicle / axon / serine-type endopeptidase activity / synapse ...zymogen activation / exocytosis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / synaptic cleft / terminal bouton / peptidase activity / cytoplasmic vesicle / axon / serine-type endopeptidase activity / synapse / dendrite / proteolysis / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Ozhogina, O.A. | ||||||
![]() | ![]() Title: NMR Solution Structure of the Neurotrypsin Kringle Domain Authors: Ozhogina, O.A. / Grishaev, A. / Bominaar, E.L. / Llinas, M. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 29.8 KB | Display | ![]() |
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PDB format | ![]() | 22.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 243.8 KB | Display | ![]() |
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Full document | ![]() | 243.6 KB | Display | |
Data in XML | ![]() | 2.9 KB | Display | |
Data in CIF | ![]() | 3.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2k4rC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 8542.461 Da / Num. of mol.: 1 Fragment: KRINGLE DOMAIN, NT/K, sequence database residues 84-160 Source method: isolated from a genetically manipulated source Details: FORMULA MASS: 8533 Da (NATURAL ABUNDANCE), 8635 Da (15N-ENRICHED), EXTINCTION COEFFICIENT (280 nm): 30855 M-1cm-1 Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q99JC8, UniProt: G3V801*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: CHEMICAL SHIFT REFERENCE: 1,4-DIOXANE, 3.75 PPM, SPECTRA USED FOR NOESY ASSIGNMENT AND STRUCTURE CALCULATIONS WERE: 2D [1H-1H]-NOESY (MIXING TIME OF 100 MS) AND 3D NOESY-[1H-15N]-HSQC (MIXING TIME OF 200 MS). |
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Sample preparation
Details | Contents: 1 MM [U-100% 15N] NT/K, 0.02% sodium azide, 90% H2O/10% D2O |
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Sample | Conc.: 1 mM / Component: Neurotrypsin / Isotopic labeling: [U-100% 15N] |
Sample conditions | Ionic strength: no salt / pH: 5.2 / Pressure: AMBIENT / Temperature: 300 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE AUTOMATED NOESY ASSIGNMENT AND STRUCTURE CALCULATIONS CARRIED OUT BY BACUS/CNS. FINAL STRUCTURE REFINEMENT IN AN EXPLICIT SHELL OF WATER WAS PERFORMED USING ARIA/CNS, ON THE BASIS OF ...Details: THE AUTOMATED NOESY ASSIGNMENT AND STRUCTURE CALCULATIONS CARRIED OUT BY BACUS/CNS. FINAL STRUCTURE REFINEMENT IN AN EXPLICIT SHELL OF WATER WAS PERFORMED USING ARIA/CNS, ON THE BASIS OF FIXED UNAMBIGUOUS DISTANCE RESTRAINTS AND STRUCTURES OBTAINED WITH BACUS/CNS, AND RESTRAINTS ON DIHEDRAL ANGLES AND HYDROGEN BONDS. NOTE THAT RESIDUES 1 - 7 AT THE N-TERMINUS AND RESIDUES 73 - 77 AT THE C-TERMINUS ARE DISORDERED. | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1342 / NOE intraresidue total count: 613 / NOE long range total count: 295 / NOE medium range total count: 119 / NOE sequential total count: 313 / Disulfide bond constraints total count: 3 / Hydrogen bond constraints total count: 24 / Protein chi angle constraints total count: 48 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 9 | ||||||||||||||||||||||||
NMR representative | Selection criteria: conformer with the lowest rmsd to the mean coordinates of the ensemble | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURE WITH THE LOWEST RMSD TO THE MEAN COORDINATES OF THE ENSEMBLE Conformers calculated total number: 70 / Conformers submitted total number: 1 |