[English] 日本語
![](img/lk-miru.gif)
- PDB-6nri: Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT83 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6nri | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of human PARP-1 ART domain bound to inhibitor UTT83 | ||||||
![]() | Poly [ADP-ribose] polymerase 1 | ||||||
![]() | transferase/transferase inhibitor / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Langelier, M.F. / Pascal, J.M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Design and Synthesis of Poly(ADP-ribose) Polymerase Inhibitors: Impact of Adenosine Pocket-Binding Motif Appendage to the 3-Oxo-2,3-dihydrobenzofuran-7-carboxamide on Potency and Selectivity. Authors: Velagapudi, U.K. / Langelier, M.F. / Delgado-Martin, C. / Diolaiti, M.E. / Bakker, S. / Ashworth, A. / Patel, B.A. / Shao, X. / Pascal, J.M. / Talele, T.T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 116.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 87.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6nrfC ![]() 6nrgC ![]() 6nrhC ![]() 6nrjC ![]() 6bhvS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30003.275 Da / Num. of mol.: 1 / Fragment: ADP-ribosyltransferase (ART) domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P09874, ![]() ![]() |
---|
-Non-polymers , 5 types, 60 molecules ![](data/chem/img/KYM.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-KYM / ( |
---|---|
#3: Chemical | ChemComp-CIT / ![]() |
#4: Chemical | ChemComp-DMS / ![]() |
#5: Chemical | ChemComp-CL / ![]() |
#6: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.55 % / Mosaicity: 0.17 ° |
---|---|
Crystal grow![]() | Temperature: 298 K / Method: evaporation / pH: 7.5 Details: ~20% PEG 3350, 0.2 M ammonium sulfate or sodium citrate, 100 mM Hepes pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 8, 2018 | ||||||||||||||||||||||||
Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (DCM), Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||
Reflection | Resolution: 2.2→48.2 Å / Num. obs: 16019 / % possible obs: 99.9 % / Redundancy: 15.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.021 / Rrim(I) all: 0.084 / Net I/σ(I): 20.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing![]() | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDBID 6BHV Resolution: 2.2→48.2 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 11.229 / SU ML: 0.139 / SU R Cruickshank DPI: 0.2204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.194 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.3 Å2 / Biso mean: 56.441 Å2 / Biso min: 37.57 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→48.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.202→2.259 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 25.1952 Å / Origin y: -4.5335 Å / Origin z: 20.062 Å
|