Research workbench
ALKBH2 F102A cross-linked to undamaged dsdna
Analyse ALKBH2 F102A cross-linked to undamaged dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MG2
- Type
- protein + DNA
- Length
- 222 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2; DNA-1; DNA-2
- EC
- 1.14.11.33
- UniProt
- Q6NS38
- Ligands
- MG
- Pockets
- 1 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2 (EC 1.14.11.33) | protein | 195 | 16% helix, 42% strand | Q6NS38 |
| B | DNA-1 | dna | 14 | — | — |
| C | DNA-2 | dna | 13 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 907 | 0.79 | 0.82 | 74 | MG |
Interfaces
3 interfaces between chains.
- B–C · 625 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- A–C · 435 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–B · 322 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 4MG2 · PDBe 4MG2 · UniProt Q6NS38
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