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- PDB-5ibj: Crystal structure Mycobacterium tuberculosis CYP121 in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ibj | |||||||||
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Title | Crystal structure Mycobacterium tuberculosis CYP121 in complex with inhibitor fragment 6 | |||||||||
![]() | Cytochrome P450 121 CYP121 | |||||||||
![]() | OXIDOREDUCTASE / Mycobacterium tuberculosis CYP121 Fragment based inhibitor screening | |||||||||
Function / homology | ![]() mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / cyclase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity / iron ion binding ...mycocyclosin synthase / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / cyclase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / carbon monoxide binding / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / oxidoreductase activity / iron ion binding / heme binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Levy, C. | |||||||||
![]() | ![]() Title: Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors. Authors: Kavanagh, M.E. / Coyne, A.G. / McLean, K.J. / James, G.G. / Levy, C.W. / Marino, L.B. / de Carvalho, L.P. / Chan, D.S. / Hudson, S.A. / Surade, S. / Leys, D. / Munro, A.W. / Abell, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.1 KB | Display | ![]() |
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PDB format | ![]() | 73.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5edtC ![]() 5ibdC ![]() 5ibeC ![]() 5ibfC ![]() 5ibgC ![]() 5ibhC ![]() 5ibiC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 43305.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cyp121, cyp121_1, EI32_2700, ERS007657_00455, ERS007661_00083, ERS007663_02869, ERS007665_01035, ERS007670_00377, ERS007672_00334, ERS007679_00173, ERS007681_01277, ERS007703_02339, ERS007720_ ...Gene: cyp121, cyp121_1, EI32_2700, ERS007657_00455, ERS007661_00083, ERS007663_02869, ERS007665_01035, ERS007670_00377, ERS007672_00334, ERS007679_00173, ERS007681_01277, ERS007703_02339, ERS007720_01219, ERS007722_01069, ERS013447_00077, ERS013471_02812, ERS023446_00317, ERS024276_01833, ERS027644_00398, ERS027652_00994, ERS027654_01464, ERS027656_01022, ERS027659_00311, ERS027666_00100, ERS031537_01827, ERS075357_02976, ERS075361_02508, ERS075387_01689, ERS124361_02646, HX90_2763 Production host: ![]() ![]() References: UniProt: A0A0T9WNE5, UniProt: P9WPP7*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-69T / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.71 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 1.5-2.1 M ammonium sulfate and 0.1 M sodium MES or Cacodylate from pH 5.5-6.15 PH range: 5.5 -6.15 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.66 Å / Num. obs: 17231 / % possible obs: 99.7 % / Redundancy: 18 % / CC1/2: 0.994 / Rmerge(I) obs: 0.256 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 16.3 % / Rmerge(I) obs: 0.969 / Mean I/σ(I) obs: 3.9 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: INHOUSE Resolution: 2.5→29.656 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→29.656 Å
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Refine LS restraints |
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LS refinement shell |
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