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Download EndnoteBypassing a 8,5'-cyclo-2'-deoxyadenosine lesion by human DNA polymerase eta at atomic resolution
Weng, P., Gao, Y., Gregory, M.T., Wang, P., Wang, Y., Yang, W.(2018) Proc.Natl.Acad.Sci.Usa --: --
6M7T
Human DNA polymerase eta in a non-productive ternary complex with Ca2+ and dTTP oppositing cdA
- DOI: 10.2210/pdb6M7T/pdb
- Classification: TRANSFERASE/DNA
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Deposited: 2018-08-21 Released: 2018-09-12
- Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.8 Å
- R-Value Free: 0.261
- R-Value Work: 0.220
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| DNA polymerase eta | A | 435 | Homo sapiens | Mutation(s): 0 Gene Names: POLH (RAD30, RAD30A, XPV) EC: 2.7.7.7 |
Find proteins for Q9Y253 (Homo sapiens) Go to Gene View: POLH Go to UniProtKB: Q9Y253 | ||||
Entity ID: 2 | ||||
|---|---|---|---|---|
| Molecule | Chains | Length | Organism | |
| DNA (5'-D(*AP*GP*TP*GP*TP*GP*AP*G)-3') | P | 8 | Homo sapiens | |
Entity ID: 3 | ||||
|---|---|---|---|---|
| Molecule | Chains | Length | Organism | |
| DNA (5'-D(*AP*TP*(02I)P*CP*TP*CP*AP*CP*AP*CP*T)-3') | T | 11 | Homo sapiens | |
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | A | GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| CA Query on CA | A | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | Ligand Interaction | |
| TTP Query on TTP | A | THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N |  | Ligand Interaction | |
| EDO Query on EDO | A | 1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| NI Query on NI | A | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| 02I Query on 02I | T | DNA LINKING | C10 H12 N5 O6 P |  | -- |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.8 Å
- R-Value Free: 0.261
- R-Value Work: 0.220
- Space Group: P 21 21 21
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 65.650 | α = 90.00 |
| b = 80.930 | β = 90.00 |
| c = 140.380 | γ = 90.00 |
| Software Name | Purpose |
|---|---|
| PHENIX | phasing |
| XSCALE | data scaling |
| PHENIX | refinement |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2018-08-21
- Released Date: 2018-09-12
- Deposition Author(s): Weng, P., Gao, Y., Yang, W.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease | United States | DK036146 |
Revision History
- Version 1.0: 2018-09-12
Type: Initial release
