Research workbench
Crystal structure of human alklyadenine DNA glycosylase in a lower and higher-affinity complex with DNA
Analyse Crystal structure of human alklyadenine DNA glycosylase in a lower and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UBY
- Type
- protein + DNA
- Length
- 399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-3-methyladenine glycosylase; DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3')
- EC
- 3.2.2.21
- UniProt
- P29372
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-3-methyladenine glycosylase (EC 3.2.2.21) | protein | 204 | 23% helix, 28% strand | P29372 |
| B | DNA-3-methyladenine glycosylase (EC 3.2.2.21) | protein | 178 | 20% helix, 34% strand | P29372 |
| C | DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3') | dna | 9 | — | — |
| D | DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDC)P*TP*TP*GP*CP*CP*T)-3') | dna | 8 | — | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.55 | 0.81 | 24 | empty |
| 2 | 253 | 0.50 | 0.74 | 34 | empty |
Interfaces
4 interfaces between chains.
- A–C · 694 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–D · 406 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–D · 356 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- A–B · 308 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3UBY · Crystal structure of human alklyadenine DNA glycosylase in a lower and higher-affinity… · the same entry in another collection · chain A against A, 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 0.97
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 3UBY · PDBe 3UBY · UniProt P29372
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