Research workbench
Muty adenine glycosylase in complex with DNA containing an abasic site
Analyse Muty adenine glycosylase in complex with DNA containing an abasic site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RRS
- Type
- protein + DNA
- Length
- 366 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3'…
- EC
- 3.2.2.-
- UniProt
- P83847
- Ligands
- SF4, CA
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3' | dna | 11 | — | — |
| C | 5'-D(*TP*GP*TP*CP*CP*AP*(HPD)P*GP*TP*CP*T)-3' | dna | 10 | — | — |
| A | Muty (EC 3.2.2.-) | protein | 345 | 46% helix, 13% strand | P83847 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.74 | 0.78 | 65 | empty |
| 2 | 125 | 0.57 | 0.83 | 25 | empty |
| 3 | 136 | 0.54 | 0.82 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–A · 720 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–A · 708 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–C · 424 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1RRS · MutY adenine glycosylase in complex with DNA containing an abasic site · the same entry in another collection · chain B against B, TM-score 1.00
- P83847 · AlphaFold monomer V2.0 prediction for adenine DNA glycosylase (P83847) · 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 P83847
- Elsewhere: RCSB PDB 1RRS · PDBe 1RRS · UniProt P83847
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