[English] 日本語
![](img/lk-miru.gif)
- PDB-4dl5: Human DNA polymerase eta inserting dCMPNPP opposite the 5'G of ci... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4dl5 | ||||||
---|---|---|---|---|---|---|---|
Title | Human DNA polymerase eta inserting dCMPNPP opposite the 5'G of cisplatin crosslinked Gs (Pt-GG2). | ||||||
![]() |
| ||||||
![]() | TRANSFERASE/DNA/INHIBITOR / cisplatin / chemoresistence / translesion synthesis / human DNA polymerse eta / kinetics / molecular splint / inhibition / DNA distorsion / second TLS polymerase / nucleotidyl transfer reaction / PCNA / TRANSFERASE-DNA-INHIBITOR complex | ||||||
Function / homology | ![]() response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / regulation of DNA repair / error-prone translesion synthesis / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / cellular response to UV-C / pyrimidine dimer repair / regulation of DNA repair / error-prone translesion synthesis / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, Y. / Biertumpfel, C. / Gregory, M. / Hanaoka, F. / Hua, Y. / Yang, W. | ||||||
![]() | ![]() Title: Structural Basis for Chemoresistance to Cisplatin Mediated by DNA Polymerase eta Authors: Zhao, Y. / Biertumpfel, C. / Gregory, M.T. / Hua, Y.J. / Hanaoka, F. / Yang, W. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 118.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 806.6 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 27.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dl2C ![]() 4dl3C ![]() 4dl4C ![]() 4dl6C ![]() 4dl7C ![]() 3mr2S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48617.707 Da / Num. of mol.: 1 / Fragment: unp residues 1-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-DNA chain , 2 types, 2 molecules TP
#2: DNA chain | Mass: 3622.380 Da / Num. of mol.: 1 / Source method: obtained synthetically |
---|---|
#3: DNA chain | Mass: 2770.834 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: dCMPNPP |
-Non-polymers , 3 types, 4 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/0KX.gif)
![](data/chem/img/CPT.gif)
![](data/chem/img/0KX.gif)
![](data/chem/img/CPT.gif)
#4: Chemical | #5: Chemical | ChemComp-0KX / | #6: Chemical | ChemComp-CPT / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
---|---|
Crystal grow | Temperature: 293 K / pH: 6 Details: MES, MgCl2, PEG 2K-MME, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2010 Details: DOUBLE SI(220) CRYSTAL AND MIRROR VERTICAL FOCUSING |
Radiation | Monochromator: DOUBLE SI(220) CRYSTAL AND MIRROR VERTICAL FOCUSING Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→30 Å / Num. obs: 10069 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 64.22 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.076 / Net I/σ(I): 18.93 |
Reflection shell | Resolution: 2.92→3 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.46 / Rsym value: 0.694 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3MR2 Resolution: 2.92→30 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.69 / σ(F): 1.34 / Phase error: 26.63 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.24 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.73 Å2
| ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.92→30 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|