MolNFT v1 · #94287 · protein + DNA
S. pombe 3-methyladenine DNA glycosylase-like protein MAG2 bound to damaged DNA
4HSB · Probable DNA-3-methyladenine glycosylase 2: “S. pombe 3-methyladenine DNA glycosylase-like protein MAG2 bound to damaged DNA”. X-ray diffraction, 2 pockets (best druggability 0.66). MolNFT v1 #94287 on GenesisL1: 3D structure…
- PDB
- 4HSB
- 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; DNA…
- EC
- 3.2.2.21
- UniProt
- O94468
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable DNA-3-methyladenine glycosylase 2 (EC 3.2.2.21) | protein | 205 | 62% helix, 0% strand | O94468 |
| B | DNA (5'-D(P*GP*GP*AP*CP*TP*(3DR)P*AP*CP*GP*GP*G)-3') | dna | 11 | — | — |
| C | DNA (5'-D(P*CP*CP*CP*GP*TP*TP*AP*GP*TP*CP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 614 | 0.66 | 0.76 | 45 | empty |
| 2 | 67 | 0.26 | 0.72 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 467 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 453 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- A–C · 407 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4HSB · S. pombe 3-methyladenine DNA glycosylase-like protein Mag2 bound to damaged DNA · 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 4HSB · PDBe 4HSB · UniProt O94468
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