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Yorodumi- PDB-6lzb: crystal structure of Human Methionine aminopeptidase (HsMetAP1b) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lzb | ||||||
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Title | crystal structure of Human Methionine aminopeptidase (HsMetAP1b) in complex with AN-P2-5H-06 | ||||||
Components | Methionine aminopeptidase 1Methionyl aminopeptidase | ||||||
Keywords | HYDROLASE / Methionine aminopeptidase | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.29 Å | ||||||
Authors | sandeep, C.B. / Addlagatta, A. | ||||||
Funding support | India, 1items
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Citation | Journal: Bioorg.Chem. / Year: 2021 Title: Selective inhibition of Helicobacter pylori methionine aminopeptidase by azaindole hydroxamic acid derivatives: Design, synthesis, in vitro biochemical and structural studies. Authors: Bala, S. / Yellamanda, K.V. / Kadari, A. / Ravinuthala, V.S.U. / Kattula, B. / Singh, O.V. / Gundla, R. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lzb.cif.gz | 153.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lzb.ent.gz | 116.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/6lzb ftp://data.pdbj.org/pub/pdb/validation_reports/lz/6lzb | HTTPS FTP |
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-Related structure data
Related structure data | 6lzcC 2b3hS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36935.926 Da / Num. of mol.: 1 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 , 6 types, 196 molecules
#2: Chemical | #3: Chemical | ChemComp-EYF / | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1M Bistris pH-6.2, 19% PEG 3350, 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9536 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 28, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9536 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.29→47.56 Å / Num. obs: 87661 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.019 / Rrim(I) all: 0.051 / Net I/σ(I): 17.9 / Num. measured all: 580633 / Scaling rejects: 85 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.423
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3H Resolution: 1.29→40.53 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1967 / WRfactor Rwork: 0.1569 / FOM work R set: 0.7978 / SU B: 2.371 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0459 / SU Rfree: 0.0474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 123.27 Å2 / Biso mean: 25.322 Å2 / Biso min: 9.1 Å2
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Refinement step | Cycle: final / Resolution: 1.29→40.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.291→1.325 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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