MolNFT v1 · #90583 · protein + DNA
Crystal structure of S. pombe ATL1 in complex with damaged DNA containing O6-carboxymethylguanine
4ENN · Alkyltransferase-like protein 1: “Crystal structure of S. pombe ATL1 in complex with damaged DNA containing O6-carboxymethylguanine”. X-ray diffraction, 3 pockets (best druggability 0.70). MolNFT v1 #90583 on GenesisL1: 3D…
- PDB
- 4ENN
- Type
- protein + DNA
- Length
- 268 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyltransferase-like protein 1; RNA (5'-R(*GP*CP*CP*AP*TP*GP*(C6G)P*CP*TP*AP*GP*TP*A)-3')
- UniProt
- Q9UTN9
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Alkyltransferase-like protein 1 | protein | 108 | 43% helix, 13% strand | Q9UTN9 |
| C, D, E, F | RNA (5'-R(*GP*CP*CP*AP*TP*GP*(C6G)P*CP*TP*AP*GP*TP*A)-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 | 750 | 0.70 | 0.77 | 50 | empty |
| 2 | 69 | 0.36 | 0.78 | 12 | empty |
| 3 | 66 | 0.33 | 0.76 | 12 | empty |
Interfaces
9 interfaces between chains.
- B–E · 747 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 724 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 392 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- E–F · 383 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- A–B · 326 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4ENN · Crystal structure of S. pombe Atl1 in complex with damaged DNA containing… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9UTN9 · AlphaFold monomer V2.0 prediction for alkyltransferase-like protein 1 (Q9UTN9) · a predicted model of the same protein · chain B 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 Q9UTN9
- Elsewhere: RCSB PDB 4ENN · PDBe 4ENN · UniProt Q9UTN9
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