MolNFT v1 · #5234 · protein + DNA
Crystal structure of the human 8-oxoguanine glycosylase (HOGG1) bound to a substrate oligonucleotide
1EBM · DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(8OG)…: “Crystal structure of the human 8-oxoguanine glycosylase (HOGG1) bound to a substrate oligonucleotide”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.60). MolNFT v1 #5234 on…
- PDB
- 1EBM
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(8OG) P*GP*TP*CP*TP*AP*CP*C)-3'); DNA (5'…
- UniProt
- O15527
- Ligands
- CA
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*GP*CP*GP*TP*CP*CP*AP*(8OG) P*GP*TP*CP*TP*AP*CP*C)-3') | dna | 15 | — | — |
| D | DNA (5'- D(*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3') | dna | 15 | — | — |
| A | 8-oxoguanine DNA glycosylase | protein | 314 | 47% helix, 11% strand | O15527 |
Ligands and binding sites
- CA · Calcium ion · metal · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.60 | 0.76 | 38 | CA |
| 2 | 80 | 0.44 | 0.80 | 16 | empty |
| 3 | 129 | 0.44 | 0.76 | 19 | empty |
| 4 | 98 | 0.32 | 0.72 | 15 | empty |
| 5 | 59 | 0.28 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- C–A · 772 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–D · 644 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- D–A · 420 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1EBM · Crystal structure of the human 8-oxoguanine glycosylase (HOGG1) bound to a substrate… · the same entry in another collection · chain C against C, 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 1EBM · PDBe 1EBM · UniProt O15527
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.