MolNFT v1 · #50200 · protein + DNA
Structure of human thymine DNA glycosylase bound to abasic and undamaged DNA
2RBA · G/T mismatch-specific thymine DNA glycosylase: “Structure of human thymine DNA glycosylase bound to abasic and undamaged DNA”. X-ray diffraction, 5 pockets (best druggability 0.82). MolNFT v1 #50200 on GenesisL1: 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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