Research workbench
Crystal structure of S. pombe ATL1 in complex with damaged DNA containing 2,6-diaminopurine
Analyse Crystal structure of S. pombe ATL1 in complex with damaged DNA containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HDV
- Type
- protein + DNA
- Length
- 134 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyltransferase-like protein 1; 5'-D(*GP*CP*CP*AP*TP*GP*(1AP)P*CP*TP*AP*GP*TP*A)-3'…
- UniProt
- Q9UTN9
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkyltransferase-like protein 1 | protein | 108 | 44% helix, 8% strand | Q9UTN9 |
| B | 5'-D(*GP*CP*CP*AP*TP*GP*(1AP)P*CP*TP*AP*GP*TP*A)-3' | dna | 13 | — | — |
| C | 5'-D(*CP*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*G)-3' | dna | 13 | — | — |
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 | 338 | 0.58 | 0.77 | 33 | empty |
| 2 | 64 | 0.33 | 0.77 | 13 | empty |
| 3 | 55 | 0.29 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 654 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 527 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–C · 443 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4HDV · Crystal structure of S. pombe ATL1 in complex with damaged DNA containing… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UTN9 · AlphaFold monomer V2.0 prediction for alkyltransferase-like protein 1 (Q9UTN9) · 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 Q9UTN9
- Elsewhere: RCSB PDB 4HDV · PDBe 4HDV · UniProt Q9UTN9
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