Research workbench
Structure determination of DNA methylation lesions N1-mea and N3-mec in duplex DNA using a cross-linked host-guest system
Analyse Structure determination of DNA methylation lesions N1-mea and N3-mec in duplex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H8R
- Type
- protein + DNA
- Length
- 230 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2…
- EC
- 1.14.11.-
- UniProt
- Q6NS38
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2 (EC 1.14.11.-) | protein | 204 | 19% helix, 40% strand | Q6NS38 |
| B | 5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*(6MA)P*GP*CP*G)-3' | dna | 13 | — | — |
| C | 5'-D(*TP*CP*GP*CP*TP*AP*TP*AP*AP*TP*AP*CP*A)-3' | dna | 13 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.73 | 0.81 | 43 | empty |
| 2 | 299 | 0.52 | 0.75 | 24 | empty |
| 3 | 56 | 0.43 | 0.83 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 681 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 583 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 581 Ų buried · 40 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3H8R · Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NS38 · AlphaFold monomer V2.0 prediction for DNA oxidative demethylase ALKBH2 (Q6NS38) · a predicted model of the same protein · chain A 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 Q6NS38
- Elsewhere: RCSB PDB 3H8R · PDBe 3H8R · UniProt Q6NS38
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