Research workbench
Crystal structure of human ABH2 bound to dsdna containing 1MEA through cross-linking away from active site
Analyse Crystal structure of human ABH2 bound to dsdna containing 1MEA through… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BTY
- Type
- protein + DNA
- Length
- 226 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7) P*DAP*DCP*DTP*DGP*DCP*DG)-3'); DNA (5'…
- EC
- 1.14.11.-
- UniProt
- Q6NS38
- Ligands
- XL3
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7) P*DAP*DCP*DTP*DGP*DCP*DG)-3') | dna | 13 | — | — |
| C | DNA (5'- D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3') | dna | 13 | — | — |
| A | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2 (EC 1.14.11.-) | protein | 200 | 18% helix, 41% strand | Q6NS38 |
Ligands and binding sites
- XL3 · propane-1-thiol · ligand · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.73 | 0.82 | 40 | XL3 |
| 2 | 296 | 0.56 | 0.77 | 22 | empty |
| 3 | 77 | 0.43 | 0.81 | 17 | empty |
| 4 | 59 | 0.29 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- B–A · 698 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–A · 612 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 532 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 3BTY · Crystal structure of human ABH2 bound to dsDNA containing 1meA through cross-linking away… · the same entry in another collection · chain B against B, 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 3BTY · PDBe 3BTY · UniProt Q6NS38
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.