MolNFT v1 · #123873 · protein + DNA
Enzyme-substrate complex of tdg catalytic domain bound to a G/U analog
5JXY · G/T mismatch-specific thymine DNA glycosylase: “Enzyme-substrate complex of tdg catalytic domain bound to a G/U analog”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #123873 on GenesisL1: 3D structure, binding…
- PDB
- 5JXY
- Type
- protein + DNA
- Length
- 252 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G/T mismatch-specific thymine DNA glycosylase; DNA (28-mer)
- EC
- 3.2.2.29
- UniProt
- Q13569
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.29) | protein | 196 | 42% helix, 13% strand | Q13569 |
| C | DNA (28-mer) | dna | 28 | — | — |
| D | DNA (28-mer) | dna | 28 | — | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.69 | 0.77 | 35 | empty |
| 2 | 197 | 0.54 | 0.79 | 18 | empty |
| 3 | 114 | 0.42 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1222 Ų buried · 121 hydrogen bonds · nucleic-nucleic
- A–D · 839 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–C · 399 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5JXY · Enzyme-substrate complex of TDG catalytic domain bound to a G/U analog · 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 5JXY · PDBe 5JXY · UniProt Q13569
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