MolNFT v1 · #59303 · protein + DNA
Crystal structure of human ABH2 cross-linked to dsdna with cofactors
3BU0 · Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2: “Crystal structure of human ABH2 cross-linked to dsdna with cofactors”. X-ray diffraction, 2 ligands (AKG, MN), 3 pockets (best druggability 0.75). MolNFT v1 #59303 on…
- PDB
- 3BU0
- Type
- protein + DNA
- Length
- 229 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2; DNA…
- EC
- 1.14.11.-
- UniProt
- Q6NS38
- Ligands
- AKG, MN
- Pockets
- 3 · best druggability 0.75
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 | 203 | 19% helix, 40% strand | Q6NS38 |
| B | DNA (5'-D(*CP*TP*GP*TP*AP*TP*(2YR)P*AP*TP*TP*GP*CP*G)-3') | dna | 13 | — | — |
| C | DNA (5'- D(*DTP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DAP*DTP*DAP*DCP*DA)-3') | dna | 13 | — | — |
Ligands and binding sites
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 | 592 | 0.75 | 0.82 | 44 | empty |
| 2 | 326 | 0.55 | 0.75 | 24 | empty |
| 3 | 66 | 0.42 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 691 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 669 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 574 Ų buried · 48 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3BU0 · crystal structure of human ABH2 cross-linked to dsDNA with 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 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 3BU0 · PDBe 3BU0 · UniProt Q6NS38
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