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- PDB-5fpr: Structure of Bacterial DNA Ligase with small-molecule ligand pyri... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5fpr | ||||||
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Title | Structure of Bacterial DNA Ligase with small-molecule ligand pyrimidin-2-amine (AT371) in an alternate binding site. | ||||||
![]() | DNA LIGASE | ||||||
![]() | LIGASE / ANTIBIOTIC DESIGN / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT371. | ||||||
Function / homology | ![]() DNA ligase (NAD+) / DNA ligase (NAD+) activity / base-excision repair, DNA ligation / DNA replication / DNA binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jhoti, H. / Ludlow, R.F. / Pathuri, P. / Saini, H.K. / Tickle, I.J. / Tisi, D. / Verdonk, M. / Williams, P.A. | ||||||
![]() | ![]() Title: Detection of Secondary Binding Sites in Proteins Using Fragment Screening. Authors: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H. #1: ![]() Title: Fragment-Based Discovery of 6-Azaindazoles as Inhibitors of Bacterial DNA Ligase. Authors: Howard, S. / Amin, N. / Benowitz, A.B. / Chiarparin, E. / Cui, H. / Deng, X. / Heightman, T.D. / Holmes, D.J. / Hopkins, A. / Huang, J. / Jin, Q. / Kreatsoulas, C. / Martin, A.C.L. / Massey, ...Authors: Howard, S. / Amin, N. / Benowitz, A.B. / Chiarparin, E. / Cui, H. / Deng, X. / Heightman, T.D. / Holmes, D.J. / Hopkins, A. / Huang, J. / Jin, Q. / Kreatsoulas, C. / Martin, A.C.L. / Massey, F. / Mccloskey, L. / Mortenson, P.N. / Pathuri, P. / Tisi, D. / Williams, P.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.2 KB | Display | ![]() |
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PDB format | ![]() | 114.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.3 KB | Display | ![]() |
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Full document | ![]() | 440.8 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5fp5C ![]() 5fp6C ![]() 5fpdC ![]() 5fpeC ![]() 5fpmC ![]() 5fpnC ![]() 5fpoC ![]() 5fpsC ![]() 5fptC ![]() 5fpyC ![]() 4cc5S C: citing same article ( 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36724.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9AIU7, DNA ligase (NAD+), DNA ligase (ATP) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-LGA / | #4: Water | ChemComp-HOH / | Nonpolymer details | PYRIMIDIN-2-AMINE (L01): ASTEX COMPOUND REGISTRY AT371. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.57 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 30, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0 Å / Relative weight: 1 |
Reflection | Resolution: 2→85.9 Å / Num. obs: 22674 / % possible obs: 98.6 % / Observed criterion σ(I): -3.7 / Redundancy: 3.4 % / Biso Wilson estimate: 23.75 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2→2.11 Å / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 7 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CC5 Resolution: 2→85.93 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9197 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.208 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.155
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Displacement parameters | Biso mean: 28.17 Å2
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Refine analyze | Luzzati coordinate error obs: 0.185 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→85.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.1 Å / Total num. of bins used: 11
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Refinement TLS params. | T13: -0.0202 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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