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- PDB-6l0u: Crystal structure of mouse glyoxalase I complexed with a small mo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6l0u | ||||||
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Title | Crystal structure of mouse glyoxalase I complexed with a small molecule inhibitor | ||||||
![]() | Lactoylglutathione lyase | ||||||
![]() | LYASE/LYASE INHIBITOR / mouse glyoxalase I / inhibitor / LYASE / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | ![]() Pyruvate metabolism / lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding ...Pyruvate metabolism / lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / methylglyoxal metabolic process / glutathione metabolic process / osteoclast differentiation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / zinc ion binding / nucleoplasm / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, L.L. / Zhou, L. | ||||||
![]() | ![]() Title: Crystal structure of mouse glyoxalase I complexed with a small molecule inhibitor Authors: Jiang, L.L. / Zhou, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.5 KB | Display | ![]() |
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PDB format | ![]() | 65.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2za0S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE
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Components
#1: Protein | Mass: 20278.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-E1L / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M MES pH 6.0, 12% (w/v) PEG2000, 16% v/v 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→50 Å / Num. obs: 25098 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Χ2: 0.663 / Net I/σ(I): 5.3 / Num. measured all: 167399 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZA0 Resolution: 1.95→23.16 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.82 Å2 / Biso mean: 41.79 Å2 / Biso min: 18.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→23.16 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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