Structure 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.
Experimental Data Snapshot
Starting Model: experimental
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wwPDB Validation   3D Report Full Report
Entity ID: 3 | |||||
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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 | |||||
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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 | |||||
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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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Ligands 4 Unique | |||||
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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 |
Length ( Å ) | Angle ( ˚ ) |
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a = 68.868 | α = 90 |
b = 148.754 | β = 90 |
c = 93.086 | γ = 90 |
Software Name | Purpose |
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ADSC | data collection |
HKL-2000 | data reduction |
MLPHARE | phasing |
CNS | refinement |
HKL-2000 | data scaling |