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Open data
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Basic information
Entry | Database: PDB / ID: 2kyt | ||||||
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Title | Solution structure of the H-REV107 N-terminal domain | ||||||
![]() | Group XVI phospholipase A2 | ||||||
![]() | HYDROLASE / H-REV107 / tumor suppressor / phospholipase / N-terminal domain | ||||||
Function / homology | ![]() membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity ...membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / peroxisome organization / N-acyltransferase activity / phospholipid biosynthetic process / phospholipase A2 activity / lens fiber cell differentiation / phospholipase A2 / peroxisomal membrane / triglyceride metabolic process / acyltransferase activity / localization / phospholipid metabolic process / lipid catabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / mitochondrial membrane / response to bacterium / peroxisome / nuclear envelope / lysosome / lysosomal membrane / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
![]() | Ren, X. / Xia, B. | ||||||
![]() | ![]() Title: Solution structure of the N-terminal catalytic domain of human H-REV107--a novel circular permutated NlpC/P60 domain Authors: Ren, X. / Lin, J. / Jin, C. / Xia, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 767.5 KB | Display | ![]() |
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PDB format | ![]() | 643.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 353.4 KB | Display | ![]() |
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Full document | ![]() | 462.3 KB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 59.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 13966.923 Da / Num. of mol.: 1 / Fragment: UNP residues 1-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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: 1 mM [U-13C; U-15N] H-REV107N-1, 30 mM sodium phosphate-2, 30 mM sodium chloride-3, 10 mM DTT-4, 90 % H2O-5, 10 % D2O-6, 0.05 w/v sodium azide-7, 0.02 w/v DSS-8, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 60 / pH: 7.0 / Pressure: ambient atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 3484 / NOE intraresidue total count: 1317 / NOE long range total count: 543 / NOE medium range total count: 315 / NOE sequential total count: 655 | ||||||||||||||||||||||||||||||||||||||||||||||||
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 / Representative conformer: 1 |