Research workbench
Acetate-free structure of the enzyme-product complex resulting from tdg action on a gu mismatch
Analyse Acetate-free structure of the enzyme-product complex resulting from tdg action… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Z3A
- 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 0.78
Structure
x-ray diffraction · 3 distinct chains · 42% 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 | 42% helix, 14% strand | Q13569 |
| C | DNA (28-mer) | dna | 28 | — | — |
| D | DNA (28-mer) | dna | 27 | — | — |
Ligands and binding sites
- ORP · 2-deoxy-5-phosphono-ribose · ligand · chains A, D
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 | 268 | 0.78 | 0.91 | 42 | ORP |
| 2 | 615 | 0.70 | 0.78 | 38 | empty |
| 3 | 108 | 0.42 | 0.77 | 23 | empty |
| 4 | 55 | 0.36 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1229 Ų buried · 130 hydrogen bonds · nucleic-nucleic
- A–D · 747 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 620 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4Z3A · Acetate-free structure of the enzyme-product complex resulting from TDG action on a GU… · 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 4Z3A · PDBe 4Z3A · UniProt Q13569
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