Research workbench
Leucine-272-alanine uracil-DNA glycosylase bound to abasic site- containing DNA
Analyse Leucine-272-alanine uracil-DNA glycosylase bound to abasic site- containing DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2SSP
- Type
- protein + DNA
- Length
- 244 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*TP*GP*TP*(AAB)P*AP*TP*CP*TP*T)-3'); DNA…
- EC
- 3.2.2.3
- UniProt
- P13051
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*CP*TP*GP*TP*(AAB)P*AP*TP*CP*TP*T)-3') | dna | 10 | — | — |
| B | DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*AP*G)-3') | dna | 11 | — | — |
| E | Protein (uracil-DNA glycosylase) (EC 3.2.2.3) | protein | 223 | 41% helix, 11% strand | P13051 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.48 | 0.73 | 27 | empty |
| 2 | 116 | 0.41 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–E · 570 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 446 Ų buried · 38 hydrogen bonds · nucleic-nucleic
- B–E · 204 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2SSP · Leucine-272-alanine uracil-DNA glycosylase bound to abasic site-containing DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P13051 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P13051) · a predicted model of the same protein · chain E against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P13051
- Elsewhere: RCSB PDB 2SSP · PDBe 2SSP · UniProt P13051
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