Research workbench
Alka undamaged DNA complex: interrogation of a G*:C base pair
Analyse Alka undamaged DNA complex: interrogation of a G*:C base pair in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OGD
- Type
- protein + DNA
- Length
- 306 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-3-methyladenine glycosylase 2; 5'-D(*GP*CP*AP*GP*TP*CP*AP*TP*G)-3'…
- EC
- 3.2.2.21
- UniProt
- P04395
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-3-methyladenine glycosylase 2 (EC 3.2.2.21) | protein | 288 | 48% helix, 13% strand | P04395 |
| B | 5'-D(*GP*CP*AP*GP*TP*CP*AP*TP*G)-3' | dna | 9 | — | — |
| C | 5'-D(*CP*AP*(BRU)P*GP*AP*CP*(BRU)P*GP*C)-3' | dna | 9 | — | — |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 387 | 0.69 | 0.81 | 36 | empty |
| 2 | 160 | 0.54 | 0.80 | 29 | empty |
| 3 | 276 | 0.54 | 0.76 | 20 | empty |
| 4 | 99 | 0.50 | 0.82 | 18 | empty |
| 5 | 94 | 0.38 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 422 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- A–B · 342 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 214 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3OGD · AlkA Undamaged DNA Complex: Interrogation of a G*:C base pair · the same entry in another collection · chain A against A, TM-score 1.00
- P04395 · AlphaFold monomer V2.0 prediction for DNA-3-methyladenine glycosylase 2 (P04395) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P04395
- Elsewhere: RCSB PDB 3OGD · PDBe 3OGD · UniProt P04395
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