MolNFT v1 · #14256 · protein + DNA
Crystal structure of HOGG1 D268E mutant with product oligonucleotide
1M3H · 5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3': “Crystal structure of HOGG1 D268E mutant with product oligonucleotide”. X-ray diffraction, 1 ligand (CA), 4 pockets (best druggability 0.58). MolNFT v1 #14256 on GenesisL1: 3D…
- PDB
- 1M3H
- Type
- protein + DNA
- Length
- 344 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3'…
- EC
- 3.2.2.-
- UniProt
- O15527
- Ligands
- CA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 5'-D(P*GP*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*GP*C)-3' | dna | 15 | — | — |
| C | 5'-D(P*GP*CP*GP*TP*CP*CP*AP*(DDX))-3' | dna | 8 | — | — |
| D | 5'-D(P*GP*TP*CP*TP*AP*CP*C)-3' | dna | 7 | — | — |
| A | 8-oxoguanine DNA glycosylase (EC 3.2.2.-) | protein | 314 | 47% helix, 12% strand | O15527 |
Ligands and binding sites
- CA · Calcium ion · metal · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.58 | 0.75 | 36 | CA |
| 2 | 176 | 0.49 | 0.77 | 30 | empty |
| 3 | 74 | 0.43 | 0.81 | 17 | empty |
| 4 | 73 | 0.28 | 0.73 | 11 | empty |
Interfaces
6 interfaces between chains.
- B–A · 450 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–A · 375 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–A · 354 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 323 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- B–D · 309 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1M3H · Crystal Structure of Hogg1 D268E Mutant with Product Oligonucleotide · the same entry in another collection · chain B against B, 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 1M3H · PDBe 1M3H · UniProt O15527
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.