MolNFT v1 · #39815 · protein + DNA
Structure of HOGG1 crosslinked to DNA sampling a normal G adjacent to an oxog
2I5W · 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*A)-3': “Structure of HOGG1 crosslinked to DNA sampling a normal G adjacent to an oxog”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.70). MolNFT v1 #39815 on GenesisL1: 3D…
- PDB
- 2I5W
- Type
- protein + DNA
- Length
- 333 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*A)-3'; 5'-D(P*CP*CP*AP*GP*(G42)P*TP*CP*TP*AP*C)-3'…
- EC
- 3.2.2.-, 4.2.99.18
- UniProt
- O15527
- Ligands
- CA
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | 5'-D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*A)-3' | dna | 12 | — | — |
| F | 5'-D(P*CP*CP*AP*GP*(G42)P*TP*CP*TP*AP*C)-3' | dna | 10 | — | — |
| A | N-GLYCOSYLASE/DNA lyase (EC 3.2.2.-, 4.2.99.18) | protein | 311 | 48% helix, 12% strand | O15527 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 405 | 0.70 | 0.82 | 41 | empty |
| 2 | 400 | 0.62 | 0.78 | 32 | empty |
| 3 | 178 | 0.51 | 0.77 | 26 | empty |
| 4 | 81 | 0.49 | 0.83 | 17 | GOL |
| 5 | 54 | 0.25 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- E–F · 505 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- F–A · 445 Ų buried · 12 hydrogen bonds · protein-nucleic
- E–A · 391 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2I5W · Structure of hOGG1 crosslinked to DNA sampling a normal G adjacent to an oxoG · the same entry in another collection · chain E against E, TM-score 1.00
- O15527 · AlphaFold monomer V2.0 prediction for N-GLYCOSYLASE/DNA lyase (O15527) · 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 O15527
- Elsewhere: RCSB PDB 2I5W · PDBe 2I5W · UniProt O15527
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