Research workbench
Structure of human thymine DNA glycosylase bound to abasic and undamaged DNA
Analyse Structure of human thymine DNA glycosylase bound to abasic and undamaged DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RBA
- Type
- protein + DNA
- Length
- 410 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G/T mismatch-specific thymine DNA glycosylase; DNA (5'…
- EC
- 3.2.2.-
- UniProt
- Q13569
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-) | protein | 182 | 37% helix, 14% strand | Q13569 |
| C | DNA (5'- D(*DCP*DAP*DGP*DCP*DTP*DCP*DTP*DGP*DTP*DAP*DCP*DGP*DTP*DGP*DAP*DGP*DC P*DAP*DGP*DTP*DGP*DGP*DA)-3') | dna | 23 | — | — |
| D | DNA (5'-D(*DCP*DCP*DAP*DCP*DTP*DGP*DCP*DTP*DCP*DAP*(3DR) P*DGP*DTP*DAP*DCP*DAP*DGP*DAP*DGP*DCP*DTP*DGP*DT)-3') | dna | 23 | — | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.82 | 0.88 | 49 | empty |
| 2 | 629 | 0.65 | 0.75 | 32 | empty |
| 3 | 166 | 0.41 | 0.74 | 27 | empty |
| 4 | 154 | 0.40 | 0.73 | 21 | empty |
| 5 | 59 | 0.40 | 0.81 | 15 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1036 Ų buried · 88 hydrogen bonds · nucleic-nucleic
- A–D · 714 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 424 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 409 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–D · 329 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2RBA · Structure of Human Thymine DNA Glycosylase Bound to Abasic and Undamaged DNA · the same entry in another collection · chain A against A, TM-score 1.00
- Q13569 · AlphaFold monomer V2.0 prediction for G/T mismatch-specific thymine DNA glycosylase… · a predicted model of the same protein · chain A 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 Q13569
- Elsewhere: RCSB PDB 2RBA · PDBe 2RBA · UniProt Q13569
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