MolNFT v1 · #81361 · protein + DNA
Crystal structure of human thymine DNA glycosylase bound to substrate analog 2'-deoxy-2'-beta-fluoro-cytidine
3UOB · 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP…: “Crystal structure of human thymine DNA glycosylase bound to substrate analog 2'-deoxy-2'-beta-fluoro-cytidine”. X-ray diffraction, 5 pockets (best druggability 0.83).…
- PDB
- 3UOB
- Type
- protein + DNA
- Length
- 399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP *GP*TP*GP*GP*A)-3'…
- EC
- 3.2.2.29
- UniProt
- Q13569
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*CP*AP*GP*CP*TP*CP*TP*GP*TP*AP*CP*GP*TP*GP*AP*GP*CP*AP *GP*TP*GP*GP*A)-3' | dna | 23 | — | — |
| D | 5'-D(*CP*CP*AP*CP*TP*GP*CP*TP*CP*AP*(1FC) P*GP*TP*AP*CP*AP*GP*AP*GP*CP*TP*GP*T)-3' | dna | 23 | — | — |
| A | G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.29) | protein | 181 | 39% helix, 15% strand | Q13569 |
| B | G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.29) | protein | 172 | 42% helix, 14% strand | Q13569 |
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 | 861 | 0.83 | 0.86 | 66 | empty |
| 2 | 694 | 0.68 | 0.76 | 34 | empty |
| 3 | 157 | 0.40 | 0.73 | 17 | empty |
| 4 | 101 | 0.33 | 0.73 | 13 | empty |
| 5 | 74 | 0.31 | 0.74 | 12 | empty |
Interfaces
6 interfaces between chains.
- C–D · 948 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- D–A · 842 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–A · 379 Ų buried · 4 hydrogen bonds · protein-nucleic
- C–B · 293 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–B · 289 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3UOB · Crystal structure of Human Thymine DNA Glycosylase Bound to Substrate Analog… · the same entry in another collection · chain C against C, 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 3UOB · PDBe 3UOB · UniProt Q13569
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