Research workbench
Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (MAG1) in complex with abasic-DNA.
Analyse Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (MAG1) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S6I
- Type
- protein + DNA
- Length
- 456 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-3-methyladenine glycosylase 1; (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3')…
- EC
- 3.2.2.21
- UniProt
- Q92383
- Ligands
- NA
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-3-methyladenine glycosylase 1 (EC 3.2.2.21) | protein | 206 | 62% helix, 0% strand | Q92383 |
| B, E | (5'-D(*TP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*T)-3') | dna | 11 | — | — |
| C | (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3') | dna | 11 | — | — |
| D | DNA-3-methyladenine glycosylase 1 (EC 3.2.2.21) | protein | 207 | 60% helix, 0% strand | Q92383 |
| F | (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.70 | 0.76 | 75 | empty |
| 2 | 446 | 0.67 | 0.79 | 50 | empty |
| 3 | 73 | 0.46 | 0.83 | 18 | empty |
| 4 | 63 | 0.39 | 0.80 | 16 | empty |
| 5 | 80 | 0.38 | 0.78 | 15 | empty |
Interfaces
9 interfaces between chains.
- D–E · 614 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 612 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 466 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–C · 444 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–F · 411 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3S6I · Schizosaccaromyces pombe 3-methyladenine DNA glycosylase (Mag1) in complex with… · the same entry in another collection · chain F against F, TM-score 1.00
- Q92383 · AlphaFold monomer V2.0 prediction for DNA-3-methyladenine glycosylase 1 (Q92383) · a predicted model of the same protein · chain D 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 Q92383
- Elsewhere: RCSB PDB 3S6I · PDBe 3S6I · UniProt Q92383
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.