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- PDB-7a13: CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a13 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN METHIONINE AMINOPEPTIDASE-2 IN COMPLEX WITH AN INHIBITOR GSK1978537A (COMPOUND 27) | ||||||
![]() | Methionine aminopeptidase 2 | ||||||
![]() | HYDROLASE / METHIONINE AMINOPEPTIDASE-2 | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thorpe, J.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.8 KB | Display | ![]() |
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PDB format | ![]() | 70.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7a12C ![]() 7a14C ![]() 7a15C ![]() 7a16C ![]() 2oazS S: Starting model for refinement 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
#1: Protein | Mass: 41510.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-QW5 / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.28 % |
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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: ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jan 22, 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: 2.04→29.97 Å / Num. all: 204045 / Num. obs: 28740 / % possible obs: 99.7 % / Redundancy: 7.1 % / Biso Wilson estimate: 25.49 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.017 / Rrim(I) all: 0.046 / Net I/σ(I): 31.7 |
Reflection shell | Resolution: 2.04→2.114 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 12.4 / Num. unique obs: 25060 / Rpim(I) all: 0.056 / Rrim(I) all: 0.148 / % possible all: 98.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2OAZ Resolution: 2.04→29.97 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.17 / SU Rfree Blow DPI: 0.141 / SU Rfree Cruickshank DPI: 0.135
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Displacement parameters | Biso max: 135.35 Å2 / Biso mean: 32.22 Å2 / Biso min: 12.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→29.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.12 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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