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Yorodumi- PDB-4u6c: HsMetAP in complex with [(1R)-1-amino-3-cyclopentylpropyl]phospho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u6c | ||||||
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Title | HsMetAP in complex with [(1R)-1-amino-3-cyclopentylpropyl]phosphonic acid | ||||||
Components | Methionine aminopeptidase 1 | ||||||
Keywords | HYDROLASE | ||||||
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 / protein maturation / aminopeptidase activity / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade ...N-terminal protein amino acid modification / peptidyl-methionine modification / initiator methionyl aminopeptidase activity / methionyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / protein maturation / aminopeptidase activity / platelet aggregation / Inactivation, recovery and regulation of the phototransduction cascade / regulation of translation / proteolysis / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.91 Å | ||||||
Authors | Arya, T. / Addlagatta, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2015 Title: Identification of the Molecular Basis of Inhibitor Selectivity between the Human and Streptococcal Type I Methionine Aminopeptidases Authors: Arya, T. / Reddi, R. / Kishor, C. / Ganji, R.J. / Bhukya, S. / Gumpena, R. / McGowan, S. / Drag, M. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u6c.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u6c.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 4u6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u6c_validation.pdf.gz | 455.2 KB | Display | wwPDB validaton report |
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Full document | 4u6c_full_validation.pdf.gz | 457.1 KB | Display | |
Data in XML | 4u6c_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 4u6c_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/4u6c ftp://data.pdbj.org/pub/pdb/validation_reports/u6/4u6c | HTTPS FTP |
-Related structure data
Related structure data | 4u1bC 4u69C 4u6eC 4u6jC 4u6wC 4u6zC 4u70C 4u71C 4u73C 4u75C 4u76C 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34454.207 Da / Num. of mol.: 1 / Fragment: UNP residues 81-386 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: METAP1, KIAA0094 / Production host: Escherichia coli (E. coli) / References: UniProt: P53582, methionyl aminopeptidase |
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-Non-polymers , 5 types, 143 molecules
#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-Q06 / [( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.87 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 2000, potassium chloride, hepes, sodium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K PH range: 5.6 - 6.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→22.64 Å / Num. obs: 26672 / % possible obs: 95.5 % / Redundancy: 3.2 % / Net I/σ(I): 2.94 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.91→21 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.237 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.141 / 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: 41.04 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→21 Å
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Refine LS restraints |
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