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Yorodumi- PDB-2edi: Solution structure of the UQ_con domain from human NEDD8-conjugat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2edi | ||||||
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Title | Solution structure of the UQ_con domain from human NEDD8-conjugating enzyme NCE2 | ||||||
Components | NEDD8-conjugating enzyme UBE2F | ||||||
Keywords | LIGASE / non-proline cis peptide bond / E2 Conjugating Enzyme / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information NEDD8 conjugating enzyme activity / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / protein neddylation / NEDD8 ligase activity / post-translational protein modification / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Endo, H. / Izumi, K. / Yoshida, M. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the UQ_con domain from human NEDD8-conjugating enzyme NCE2 Authors: Endo, H. / Izumi, K. / Yoshida, M. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2edi.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2edi.ent.gz | 881.4 KB | Display | PDB format |
PDBx/mmJSON format | 2edi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/2edi ftp://data.pdbj.org/pub/pdb/validation_reports/ed/2edi | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 19506.961 Da / Num. of mol.: 1 / Fragment: UQ_con Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: NCE2 / Plasmid: P050314-14 References: UniProt: Q969M7, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.62mM 13C,15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT ; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 10% D2O, 90% H2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |