MolNFT v1 · #59315 · protein + DNA
X-ray structure of human ABH2 bound to dsdna with MN(II) and 2KG
3BUC · DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)…: “X-ray structure of human ABH2 bound to dsdna with MN(II) and 2KG”. X-ray diffraction, 3 ligands (XL3, AKG, MN), 4 pockets (best druggability 0.73). MolNFT v1 #59315 on GenesisL1: 3D…
- PDB
- 3BUC
- 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, AKG, MN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 20% 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 | 20% helix, 41% strand | Q6NS38 |
Ligands and binding sites
- XL3 · propane-1-thiol · ligand · chains B, C, A
- AKG · 2-oxoglutaric acid · ligand · chains B, A
- MN · Manganese (II) ion · metal · chains B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.73 | 0.81 | 37 | XL3 |
| 2 | 50 | 0.70 | 0.98 | 19 | MN, AKG |
| 3 | 257 | 0.53 | 0.77 | 23 | empty |
| 4 | 64 | 0.43 | 0.82 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–A · 694 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–A · 577 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 526 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 3BUC · X-ray structure of human ABH2 bound to dsDNA with Mn(II) and 2KG · 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 3BUC · PDBe 3BUC · UniProt Q6NS38
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