Research workbench
Crystal structure of the human aag DNA repair glycosylase complexed with DNA
Analyse Crystal structure of the human aag DNA repair glycosylase complexed with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F6O
- Type
- protein + DNA
- Length
- 237 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*AP*CP*AP*TP*GP*(YRR) P*TP*TP*GP*CP*CP*T)-3'); DNA (5'…
- EC
- 3.2.2.20
- UniProt
- P29372
- Ligands
- NA
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'-D(*GP*AP*CP*AP*TP*GP*(YRR) P*TP*TP*GP*CP*CP*T)-3') | dna | 13 | — | — |
| E | DNA (5'- D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3') | dna | 13 | — | — |
| A | 3-methyl-adenine DNA glycosylase (EC 3.2.2.20) | protein | 211 | 27% helix, 27% strand | P29372 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.56 | 0.81 | 19 | empty |
| 2 | 64 | 0.28 | 0.73 | 11 | empty |
| 3 | 51 | 0.27 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- D–A · 637 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–E · 522 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- E–A · 406 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1F6O · Crystal structure of the human aag DNA repair glycosylase complexed with DNA · the same entry in another collection · chain E against E, TM-score 1.00
- P29372 · AlphaFold monomer V2.0 prediction for DNA-3-methyladenine glycosylase (P29372) · 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 P29372
- Elsewhere: RCSB PDB 1F6O · PDBe 1F6O · UniProt P29372
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