Research workbench
Crystal structure of the human aag DNA repair glycosylase complexed with 1,N6-ethenoadenine-DNA
Analyse Crystal structure of the human aag DNA repair glycosylase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EWN
- Type
- protein + DNA
- Length
- 224 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*(EDA)P*TP*TP*GP*CP*C)-3'); DNA…
- EC
- 3.2.2.21
- UniProt
- P29372
- Ligands
- NA
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDA)P*TP*TP*GP*CP*C)-3') | dna | 12 | — | — |
| E | DNA (5'-D(P*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3') | dna | 12 | — | — |
| A | 3-methyl-adenine DNA glycosylase (EC 3.2.2.21) | protein | 200 | 24% helix, 29% 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
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.56 | 0.81 | 29 | empty |
Interfaces
3 interfaces between chains.
- D–A · 683 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–E · 530 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- E–A · 392 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1EWN · Crystal structure of the human aag DNA repair glycosylase complexed with… · the same entry in another collection · chain D against D, 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 1EWN · PDBe 1EWN · UniProt P29372
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