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- PDB-8b47: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b47 | |||||||||
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Title | Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a cyclic di-adenosine derivative | |||||||||
![]() | NAD kinase 1 | |||||||||
![]() | TRANSFERASE / tetrameric NAD-kinase | |||||||||
Function / homology | ![]() NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gelin, M. / Labesse, G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria. Authors: Clement, D.A. / Gelin, M. / Leseigneur, C. / Huteau, V. / Mondange, L. / Pons, J.L. / Dussurget, O. / Lionne, C. / Labesse, G. / Pochet, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.1 KB | Display | ![]() |
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PDB format | ![]() | 180.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7zz7C ![]() 7zz9C ![]() 7zzaC ![]() 7zzbC ![]() 7zzcC ![]() 7zzdC ![]() 7zzeC ![]() 7zzfC ![]() 7zzgC ![]() 7zzhC ![]() 7zzjC ![]() 8a9vC ![]() 6rg9S C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
Experimental dataset #1 | Data reference: ![]() |
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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
#1: Protein | Mass: 31045.279 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: nadK1, lmo0968 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-1PE / | #4: Chemical | #5: 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: 2.04 Å3/Da / Density % sol: 39.85 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 25 %(v/v) PEG 550 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 23, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.53→72.94 Å / Num. obs: 17576 / % possible obs: 98.7 % / Redundancy: 12.3 % / Biso Wilson estimate: 59.07 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.063 / Rrim(I) all: 0.227 / Net I/σ(I): 10.1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6RG9 Resolution: 2.53→51.39 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.13 Å2 / Biso mean: 62.511 Å2 / Biso min: 38.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.53→51.39 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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