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Yorodumi- PDB-6bb1: Lactate Dehydrogenase in complex with inhibitor (R)-5-((2-chlorop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bb1 | |||||||||
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Title | Lactate Dehydrogenase in complex with inhibitor (R)-5-((2-chlorophenyl)thio)-6'-(4-fluorophenoxy)-4-hydroxy-2-(thiophen-3-yl)-2,3-dihydro-[2,2'-bipyridin]-6(1H)-one | |||||||||
Components | L-lactate dehydrogenase A chain | |||||||||
Keywords | OXIDOREDUCTASE/Inhibitor / inhibitor / OXIDOREDUCTASE / OXIDOREDUCTASE-Inhibitor complex | |||||||||
Function / homology | Function and homology information oxidoreductase complex / lactate metabolic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion ...oxidoreductase complex / lactate metabolic process / Pyruvate metabolism / L-lactate dehydrogenase / L-lactate dehydrogenase activity / pyruvate metabolic process / substantia nigra development / glycolytic process / cadherin binding / mitochondrion / extracellular exosome / membrane / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Ultsch, M. / Eigenbrot, C. | |||||||||
Citation | Journal: To Be Published Title: Structure-guided optimization and in vivo activities of hydroxylactone and hydroxylactam Inhibitors of Human Lactate Dehydrogenase Authors: Wei, B. / Labadie, S.S. / Robarge, K. / Chen, J. / Chen, Z. / Corson, L.B. / Ding, C.Z. / DiPasquale, A.G. / Dragovich, P.S. / Eigenbrot, C. / Evangelista, M. / Fauber, B.P. / Goa, Z. / Ge, ...Authors: Wei, B. / Labadie, S.S. / Robarge, K. / Chen, J. / Chen, Z. / Corson, L.B. / Ding, C.Z. / DiPasquale, A.G. / Dragovich, P.S. / Eigenbrot, C. / Evangelista, M. / Fauber, B.P. / Goa, Z. / Ge, H. / Hitz, A. / Ho, Q. / Lai, K.W. / Liu, W. / Liu, Y. / Li, C. / Ma, S. / Malek, S. / O'Brien, T. / Pang, J. / Peterson, D. / Salphati, L. / Sideris, S. / Ultsch, M. / Yen, I. / Yue, Q. / Zhang, H. / Zhou, A. / Purkey, H.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bb1.cif.gz | 525.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bb1.ent.gz | 434.8 KB | Display | PDB format |
PDBx/mmJSON format | 6bb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/6bb1 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/6bb1 | HTTPS FTP |
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-Related structure data
Related structure data | 6badC 6bagC 6baxC 6bazC 6bb0C 6bb2C 6bb3C 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 36603.473 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDHA, PIG19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00338, L-lactate dehydrogenase |
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-Non-polymers , 5 types, 794 molecules
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-D3J / ( #5: Chemical | ChemComp-LAC / | #6: 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: 2.2 Å3/Da / Density % sol: 44.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG3350, sodium malonate |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 25, 2013 |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 110936 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 0.121 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 11116 / Rsym value: 0.679 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I10 Resolution: 2.3→48.74 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.889 / SU R Cruickshank DPI: 0.433 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.445 / SU Rfree Blow DPI: 0.241 / SU Rfree Cruickshank DPI: 0.243
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Displacement parameters | Biso mean: 41.67 Å2
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Refine analyze | Luzzati coordinate error obs: 0.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→48.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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