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Yorodumi- PDB-5d6e: Structure of human methionine aminopeptidase 2 with covalent spir... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d6e | ||||||
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Title | Structure of human methionine aminopeptidase 2 with covalent spiroepoxytriazole inhibitor (-)-31b | ||||||
Components | Methionine aminopeptidase 2 | ||||||
Keywords | HYDROLASE / Methionine aminopeptidase 2 / Spiroepoxytriazoles / inhibitor | ||||||
Function / homology | Function and homology information N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding ...N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / protein processing / Inactivation, recovery and regulation of the phototransduction cascade / RNA binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Janowski, R. / Miller, A.K. / Niessing, D. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2016 Title: Spiroepoxytriazoles Are Fumagillin-like Irreversible Inhibitors of MetAP2 with Potent Cellular Activity. Authors: Morgen, M. / Jost, C. / Malz, M. / Janowski, R. / Niessing, D. / Klein, C.D. / Gunkel, N. / Miller, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d6e.cif.gz | 188.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d6e.ent.gz | 146.9 KB | Display | PDB format |
PDBx/mmJSON format | 5d6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/5d6e ftp://data.pdbj.org/pub/pdb/validation_reports/d6/5d6e | HTTPS FTP |
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-Related structure data
Related structure data | 5clsSC 5d6fC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 41510.141 Da / Num. of mol.: 1 / Fragment: UNP residues 108-478 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METAP2, MNPEP, P67EIF2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P50579, methionyl aminopeptidase | ||||
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#2: Chemical | ChemComp-94A / ( | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: Na Citrate, Tert-butanol / PH range: 5.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0716 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0716 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50 Å / Num. obs: 73029 / % possible obs: 99.3 % / Redundancy: 4.33 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 13.94 |
Reflection shell | Resolution: 1.49→1.529 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.17 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CLS Resolution: 1.49→50 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.976 / SU B: 2.39 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.327 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→50 Å
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Refine LS restraints |
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