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Yorodumi- PDB-7a15: CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a15 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK2224863A (COMPOUND 42) | ||||||
Components | Methionine aminopeptidase 2 | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 | 7a15.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a15.ent.gz | 71.6 KB | Display | PDB format |
PDBx/mmJSON format | 7a15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a15_validation.pdf.gz | 775.2 KB | Display | wwPDB validaton report |
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Full document | 7a15_full_validation.pdf.gz | 776.7 KB | Display | |
Data in XML | 7a15_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 7a15_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/7a15 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/7a15 | HTTPS FTP |
-Related structure data
Related structure data | 7a12C 7a13C 7a14C 7a16C 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-QV5 / | #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: 2.69 Å3/Da / Density % sol: 54.35 % |
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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: Jul 2, 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: 2.15→31.67 Å / Num. all: 24256 / Num. obs: 24256 / % possible obs: 97.94 % / Redundancy: 4.7 % / Biso Wilson estimate: 23.22 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.053 / Rrim(I) all: 0.117 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.15→2.227 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2447 / Rpim(I) all: 0.248 / Rrim(I) all: 0.539 / % possible all: 99.63 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OAZ Resolution: 2.15→31.67 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.216 / SU Rfree Blow DPI: 0.168 / SU Rfree Cruickshank DPI: 0.16
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Displacement parameters | Biso max: 122.31 Å2 / Biso mean: 31.58 Å2 / Biso min: 12.31 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→31.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.25 Å / Rfactor Rfree error: 0 / Total num. of bins used: 12
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