MolNFT v1 · #115947 · protein + DNA
Structure of the enzyme-product complex resulting from tdg action on a gcac mismatch
5CYS · G/T mismatch-specific thymine DNA glycosylase: “Structure of the enzyme-product complex resulting from tdg action on a gcac mismatch”. X-ray diffraction, 1 ligand (ORP), 4 pockets (best druggability 0.75). MolNFT v1 #115947 on…
- PDB
- 5CYS
- 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
- Ligands
- ORP
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.29) | protein | 197 | 38% helix, 14% strand | Q13569 |
| C | DNA (28-mer) | dna | 28 | — | — |
| D | DNA (28-mer) | dna | 27 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.75 | 0.86 | 40 | ORP, ACY |
| 2 | 631 | 0.65 | 0.75 | 40 | empty |
| 3 | 82 | 0.37 | 0.77 | 21 | empty |
| 4 | 51 | 0.33 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1242 Ų buried · 150 hydrogen bonds · nucleic-nucleic
- A–D · 573 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 398 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5CYS · Structure of the enzyme-product complex resulting from TDG action on a GcaC mismatch · 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 5CYS · PDBe 5CYS · UniProt Q13569
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