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Yorodumi- PDB-4i9u: Crystal structure of rabbit LDHA in complex with a fragment inhib... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i9u | ||||||
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Title | Crystal structure of rabbit LDHA in complex with a fragment inhibitor AP26256 | ||||||
Components | L-lactate dehydrogenase A chain | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / cancer / fragment / inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information L-lactate dehydrogenase / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhou, T. / Kohlmann, A. / Stephan, Z.G. / Commodore, L. / Greenfield, M.T. / Zhu, X. / Dalgarno, D.C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Fragment growing and linking lead to novel nanomolar lactate dehydrogenase inhibitors. Authors: Kohlmann, A. / Zech, S.G. / Li, F. / Zhou, T. / Squillace, R.M. / Commodore, L. / Greenfield, M.T. / Lu, X. / Miller, D.P. / Huang, W.S. / Qi, J. / Thomas, R.M. / Wang, Y. / Zhang, S. / ...Authors: Kohlmann, A. / Zech, S.G. / Li, F. / Zhou, T. / Squillace, R.M. / Commodore, L. / Greenfield, M.T. / Lu, X. / Miller, D.P. / Huang, W.S. / Qi, J. / Thomas, R.M. / Wang, Y. / Zhang, S. / Dodd, R. / Liu, S. / Xu, R. / Xu, Y. / Miret, J.J. / Rivera, V. / Clackson, T. / Shakespeare, W.C. / Zhu, X. / Dalgarno, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i9u.cif.gz | 498 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i9u.ent.gz | 415.1 KB | Display | PDB format |
PDBx/mmJSON format | 4i9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i9u_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 4i9u_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 4i9u_validation.xml.gz | 101.8 KB | Display | |
Data in CIF | 4i9u_validation.cif.gz | 133.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/4i9u ftp://data.pdbj.org/pub/pdb/validation_reports/i9/4i9u | HTTPS FTP |
-Related structure data
Related structure data | 4i8xC 4i9hC 4i9nC 1i10S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 36481.375 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P13491, L-lactate dehydrogenase #2: Chemical | ChemComp-1E7 / #3: Water | ChemComp-HOH / | |
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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: 2.74 Å3/Da / Density % sol: 55.09 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris, pH 8.0, 30% PEG550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 9, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 108557 / Num. obs: 103643 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Highest resolution: 2.5 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I10 Resolution: 2.5→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 90.4 Å2 / Biso mean: 33.1914 Å2 / Biso min: 7.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Xplor file |
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