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Yorodumi- PDB-6d4r: M. thermoresistible GuaB2 delta-CBS in complex with inhibitor Com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d4r | ||||||||||||
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Title | M. thermoresistible GuaB2 delta-CBS in complex with inhibitor Compound 18 (VCC399134) | ||||||||||||
Components | Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Complex / Fragment / IMPDH / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex | ||||||||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mycobacterium thermoresistibile (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||||||||
Authors | Ascher, D.B. / Pacitto, A. / Blundell, T.L. | ||||||||||||
Funding support | European Union, United Kingdom, Australia, 3items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2019 Title: Synthesis and Structure-Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH. Authors: Singh, V. / Pacitto, A. / Donini, S. / Ferraris, D.M. / Boros, S. / Illyes, E. / Szokol, B. / Rizzi, M. / Blundell, T.L. / Ascher, D.B. / Pato, J. / Mizrahi, V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d4r.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d4r.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 6d4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/6d4r ftp://data.pdbj.org/pub/pdb/validation_reports/d4/6d4r | HTTPS FTP |
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-Related structure data
Related structure data | 6d4qC 6d4sC 6d4tC 6d4uC 6d4vC 6d4wC 5j5rS 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
#1: Protein | Mass: 39854.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium thermoresistibile (bacteria) Strain: ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316 Gene: guaB, KEK_23061 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CNL4, IMP dehydrogenase |
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#2: Chemical | ChemComp-IMP / |
#3: Chemical | ChemComp-FWY / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.14 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, calcium chloride, iso-propanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 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: 1.34→42.33 Å / Num. obs: 73343 / % possible obs: 99.9 % / Redundancy: 2 % / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.34→1.39 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J5R Resolution: 1.34→42.33 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→42.33 Å
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Refine LS restraints |
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LS refinement shell |
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