Research workbench
Unprecedented sculpting of DNA at abasic sites by DNA glycoslase homolog MAG2
Analyse Unprecedented sculpting of DNA at abasic sites by DNA glycoslase homolog MAG2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B24
- Type
- protein + DNA
- Length
- 227 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable DNA-3-methyladenine glycosylase 2; 5'-D(*GP*CP*TP*AP*CP*3DRP*TP*AP*TP*CP*GP)-3'…
- EC
- 3.2.2.21
- UniProt
- O94468
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable DNA-3-methyladenine glycosylase 2 (EC 3.2.2.21) | protein | 206 | 64% helix, 0% strand | O94468 |
| X | 5'-D(*GP*CP*TP*AP*CP*3DRP*TP*AP*TP*CP*GP)-3' | dna | 11 | — | — |
| Y | 5'-D(*CP*GP*AP*TP*AP*GP*GP*TP*AP*GP)-3' | dna | 10 | — | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.68 | 0.78 | 41 | empty |
| 2 | 50 | 0.26 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–X · 539 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–Y · 449 Ų buried · 8 hydrogen bonds · protein-nucleic
- X–Y · 446 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4B24 · Unprecedented sculpting of DNA at abasic sites by DNA glycosylase homolog Mag2 · the same entry in another collection · chain A against A, TM-score 1.00
- O94468 · AlphaFold monomer V2.0 prediction for alkylbase DNA glycosidase-like protein MAG2 (O94468) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O94468
- Elsewhere: RCSB PDB 4B24 · PDBe 4B24 · UniProt O94468
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