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Open data
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Basic information
Entry | Database: PDB / ID: 4u75 | ||||||
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Title | HsMetAP (F309M) in complex with Methionine | ||||||
![]() | Methionine aminopeptidase 1 | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Arya, T. / Addlagatta, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.6 KB | Display | ![]() |
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PDB format | ![]() | 59 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.3 KB | Display | ![]() |
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Full document | ![]() | 453.1 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4u1bC ![]() 4u69C ![]() 4u6cC ![]() 4u6eC ![]() 4u6jC ![]() 4u6wC ![]() 4u6zC ![]() 4u70C ![]() 4u71C ![]() 4u73C ![]() 4u76C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34438.230 Da / Num. of mol.: 1 / Fragment: UNP residues 81-386 / Mutation: F309M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 232 molecules ![](data/chem/img/CO.gif)
![](data/chem/img/K.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MET.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-MET / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 15% PEGMME, 100mM HEPES PH 6 / PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 19, 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: 1.93→18 Å / Num. obs: 25066 / % possible obs: 95.5 % / Redundancy: 3.1 % / Net I/σ(I): 2.64 |
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Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.94→17.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.26 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.146 / 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: 25.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→17.7 Å
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