Download MendeleyHydrogen-Bonding Capability of Difluorotoluene Nucleoside in Replication Complexes
Xia, S., Konigsberg, W.H., Wang, J.To be published.
3QEX
RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite dT
- PDB DOI: https://doi.org/10.2210/pdb3QEX/pdb
- NAKB: 3QEX
- Classification: Transferase/DNA
- Organism(s): Escherichia phage RB69, synthetic construct
- Expression System: Escherichia coli BL21
- Mutation(s): Yes
- Deposited: 2011-01-20 Released: 2012-01-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.73 Å
- R-Value Free: 0.206
- R-Value Work: 0.178
- R-Value Observed: 0.180
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DNA polymerase | 903 | Escherichia phage RB69 | Mutation(s): 5 Gene Names: 43 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt) |  | |
UniProt | |||||
Find proteins for Q38087 (Escherichia phage RB69) Explore Q38087 Go to UniProtKB: Q38087 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q38087 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*TP*CP*AP*TP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3') | B [auth T] | 18 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3') | C [auth P] | 13 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DGT Query on DGT | D [auth A] | 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-N |  | ||
| CA Query on CA | E [auth A], F [auth A], G [auth A], H [auth A], I [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.73 Å
- R-Value Free: 0.206
- R-Value Work: 0.178
- R-Value Observed: 0.180
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 74.991 | α = 90 |
| b = 120.211 | β = 90 |
| c = 130.361 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-2000 | data collection |
| AMoRE | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2012-01-25 Deposition Author(s): Xia, S., Konigsberg, W.H., Wang, J.
Revision History (Full details and data files)
- Version 1.0: 2012-01-25
Type: Initial release - Version 1.1: 2024-02-21
Changes: Data collection, Database references, Derived calculations
