MolNFT v1 · #165623 · protein + DNA
Human thymine DNA glycosylase bound to DNA with 2'-F-5-carboxyl-dc substrate analog
6U17 · G/T mismatch-specific thymine DNA glycosylase: “Human thymine DNA glycosylase bound to DNA with 2'-F-5-carboxyl-dc substrate analog”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #165623 on GenesisL1: 3D…
- PDB
- 6U17
- Type
- protein + DNA
- Length
- 253 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); DNA (30-mer)
- EC
- 3.2.2.29
- UniProt
- Q13569
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.29) | protein | 197 | 42% helix, 12% strand | Q13569 |
| C | DNA (28-mer) | dna | 28 | — | — |
| D | DNA (30-mer) | dna | 28 | — | — |
Ligands and binding sites
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 659 | 0.69 | 0.77 | 33 | empty |
| 2 | 249 | 0.67 | 0.84 | 39 | empty |
| 3 | 60 | 0.38 | 0.80 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1232 Ų buried · 119 hydrogen bonds · nucleic-nucleic
- A–D · 902 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–C · 513 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification, oxidation).
Compared structures
- 6U17 · Human thymine DNA glycosylase bound to DNA with 2'-F-5-carboxyl-dC substrate 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 0.98
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 6U17 · PDBe 6U17 · UniProt Q13569
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