Research workbench
ABH2 cross-linked with undamaged dsdna-1 containing cofactors
Analyse ABH2 cross-linked with undamaged dsdna-1 containing cofactors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3S57
- Type
- protein + DNA
- Length
- 232 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
- Ligands
- AKG, XL3, MN
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 41% 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, 41% strand | Q6NS38 |
| B | 5'-D(*CP*TP*GP*TP*CP*AP*TP*CP*AP*CP*TP*GP*CP*G)-3' | dna | 14 | — | — |
| C | 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*TP*GP*AP*CP*A)-3' | dna | 14 | — | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- XL3 · propane-1-thiol · ligand · chains A, B, C
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.81 | 0.84 | 60 | MN, AKG |
| 2 | 603 | 0.72 | 0.80 | 39 | XL3 |
Interfaces
3 interfaces between chains.
- A–C · 654 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–C · 621 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–B · 468 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3S57 · ABH2 cross-linked with undamaged dsDNA-1 containing cofactors · 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 1.00
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 3S57 · PDBe 3S57 · UniProt Q6NS38
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