MolNFT v1 · #124713 · protein + DNA
Muty N-terminal domain in complex with DNA containing an intrahelical OXOG:A base-pair
5KN9 · Adenine DNA glycosylase: “Muty N-terminal domain in complex with DNA containing an intrahelical OXOG:A base-pair”. X-ray diffraction, 2 ligands (SF4, CA), 3 pockets (best druggability 0.71). MolNFT v1 #124713 on GenesisL1: 3D…
- PDB
- 5KN9
- Type
- protein + DNA
- Length
- 242 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenine DNA glycosylase; DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3'); DNA…
- EC
- 3.2.2.-
- UniProt
- P83847
- Ligands
- SF4, CA
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenine DNA glycosylase (EC 3.2.2.-) | protein | 222 | 66% helix, 0% strand | P83847 |
| C | DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3') | dna | 10 | — | — |
| D | DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3') | dna | 10 | — | — |
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 | 583 | 0.71 | 0.79 | 54 | empty |
| 2 | 195 | 0.59 | 0.81 | 23 | empty |
| 3 | 207 | 0.54 | 0.78 | 30 | CA |
Interfaces
3 interfaces between chains.
- C–D · 505 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- A–D · 483 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 333 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 5KN9 · MutY N-terminal domain in complex with DNA containing an intrahelical oxoG:A base-pair · the same entry in another collection · chain A against A, 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 0.98
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 P83847
- Elsewhere: RCSB PDB 5KN9 · PDBe 5KN9 · UniProt P83847
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