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Yorodumi- PDB-7a16: CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a16 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2229238A (COMPOUND 43) | ||||||
Components | Methionine aminopeptidase 2Methionyl aminopeptidase | ||||||
Keywords | HYDROLASE / METHIONINE AMINOPEPTIDASE-2 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Thorpe, J.H. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2020 Title: Structure-based optimisation of orally active & reversible MetAP-2 inhibitors maintaining a tight 'molecular budget'. Authors: Hirst, D.J. / Brandt, M. / Bruton, G. / Christodoulou, E. / Cutler, L. / Deeks, N. / Goodacre, J.D. / Jack, T. / Lindon, M. / Miah, A. / Page, K. / Parr, N. / Shukla, L. / Sims, M. / Thomas, ...Authors: Hirst, D.J. / Brandt, M. / Bruton, G. / Christodoulou, E. / Cutler, L. / Deeks, N. / Goodacre, J.D. / Jack, T. / Lindon, M. / Miah, A. / Page, K. / Parr, N. / Shukla, L. / Sims, M. / Thomas, P. / Thorpe, J. / Holmes, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a16.cif.gz | 98.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a16.ent.gz | 72.1 KB | Display | PDB format |
PDBx/mmJSON format | 7a16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/7a16 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/7a16 | HTTPS FTP |
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-Related structure data
Related structure data | 7a12C 7a13C 7a14C 7a15C 2oazS 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
#1: Protein | Mass: 41510.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METAP2, MNPEP, P67EIF2 / Production host: unidentified baculovirus / References: UniProt: P50579, methionyl aminopeptidase | ||||||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-HZE / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 200mM potassium phosphate pH 7.4, 100mM MnCl2, 5mM dithiothreitol (DTT) and 25-50% 2-methyl-2,4-pentanediol (MPD) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→26.32 Å / Num. all: 159346 / Num. obs: 35729 / % possible obs: 99.04 % / Redundancy: 4.5 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 15917 / % possible all: 94.53 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OAZ Resolution: 1.9→26.32 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.125
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Displacement parameters | Biso max: 123.5 Å2 / Biso mean: 31.96 Å2 / Biso min: 13.66 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→26.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
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