Download MendeleyStructure of Family 5 Uracil-DNA Glycosylase Bound to DNA Reveals Insights into the Mechanism for Substrate Recognition and Catalysis
Kosaka, H., Nakagawa, N., Masui, R., Kuramitsu, S.To be published.
2DP6
Crystal structure of uracil-DNA glycosylase in complex with AP:C containing DNA
- PDB DOI: https://doi.org/10.2210/pdb2DP6/pdb
- NAKB: 2DP6
- Classification: HYDROLASE/DNA
- Organism(s): Thermus thermophilus HB8
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2006-05-07 Released: 2007-05-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.217
- R-Value Work: 0.204
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| uracil-DNA glycosylase | C [auth A] | 219 | Thermus thermophilus HB8 | Mutation(s): 0 Gene Names: ttUDGB EC: 3.2.2 |  |
UniProt | |||||
Find proteins for Q5SJ65 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJ65 Go to UniProtKB: Q5SJ65 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5SJ65 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*AP*TP*GP*TP*TP*GP*CP*(D1P)P*TP*TP*AP*GP*TP*CP*C)-3' | A [auth C] | 15 | N/A |  | |
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| 5'-D(*GP*GP*AP*CP*TP*AP*AP*CP*GP*CP*AP*AP*CP*A)-3' | B [auth D] | 14 | N/A |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SF4 Query on SF4 | E [auth A] | IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N |  | ||
| 2HP Query on 2HP | D, F [auth A] | DIHYDROGENPHOSPHATE ION H2 O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-M |  | ||
| GOL Query on GOL | G [auth A], H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| EOH Query on EOH | I [auth A] | ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.217
- R-Value Work: 0.204
- Space Group: C 2 2 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 68.868 | α = 90 |
| b = 148.754 | β = 90 |
| c = 93.086 | γ = 90 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| HKL-2000 | data reduction |
| MLPHARE | phasing |
| CNS | refinement |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2007-05-22 Deposition Author(s): Kosaka, H., Nakagawa, N., Masui, R., Kuramitsu, S., Hoseki, J., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Revision History (Full details and data files)
- Version 1.0: 2007-05-22
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description
