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Structure Feature
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Ligands & Environment
1JDK
pdb_00001jdk
10.2210/pdb1jdk/pdb
Download file
FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Ionic Strength
Solvent
pH
Pressure
Temprature (K)
1
2D NOESY
3mMpeptide in 500ul solvent
?
100% DMSO-D6
?
atmospheric
298
2
DQF-COSY
3mMpeptide in 500ul solvent
?
100% DMSO-D6
?
atmospheric
298
3
TOCSY
3mMpeptide in 500ul solvent
?
100% DMSO-D6
?
atmospheric
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
NMR Refinement
Method
Details
Software
torsion angle dynamics, energy minimization, molecular dynamics
50 initial random strucutre were generated using DYANA software, followed by 500 steps energy minimization. Then using DISCOVER 3 35 ps MD in vacuo at 300K, 200 steps energy minimization under NMR restraints and 750 steps conjugate gradient EM.
1
NMR Ensemble Information
Conformer Selection Criteria
target function
Conformers Calculated Total Number
50
Conformers Submitted Total Number
25
Representative Model
1 (lowest energy)
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
collection
2.6
XwinNMR
Bruker GMBH
2
processing
2.6
XwinNMR
Bruker GMBH
3
data analysis
1.2
XEASY
Bartels C., Xia T., Billeter M., Guentert P and Wuethrich K. (1995) J. Biomol.NMR, 5, 1-10
4
refinement
1.5
DYANA
Guentert P., Mumenthaler C. and Wuethrich K. (1997) J.Mol.Biol., 273,283-298
5
refinement
3
Discover
MSI, San Diego