MolNFT v1 · #86290 · protein + DNA
Unprecedented sculpting of DNA at abasic sites by DNA glycoslase homolog MAG2
4B24 · Probable DNA-3-methyladenine glycosylase 2: “Unprecedented sculpting of DNA at abasic sites by DNA glycoslase homolog MAG2”. X-ray diffraction, 2 pockets (best druggability 0.68). MolNFT v1 #86290 on GenesisL1: 3D structure, binding…
- 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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