MolNFT v1 · #78310 · protein + DNA
ABH2 cross-linked to undamaged dsdna-2 with cofactors
3S5A · Alpha-ketoglutarate-dependent dioxygenase alkb homolog 2: “ABH2 cross-linked to undamaged dsdna-2 with cofactors”. X-ray diffraction, 3 ligands (AKG, XL3, MN), 2 pockets (best druggability 0.80). MolNFT v1 #78310 on GenesisL1: 3D…
- PDB
- 3S5A
- 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 0.80
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 | 204 | 19% helix, 40% strand | Q6NS38 |
| B | 5'-D(*CP*TP*GP*TP*CP*TP*CP*AP*CP*TP*GP*TP*CP*G)-3' | dna | 14 | — | — |
| C | 5'-D(*TP*CP*GP*AP*CP*AP*GP*TP*GP*AP*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 · 3 copies · chains A, C
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 | 821 | 0.80 | 0.83 | 59 | MN, AKG |
| 2 | 767 | 0.72 | 0.78 | 41 | GOL, XL3 |
Interfaces
3 interfaces between chains.
- B–C · 613 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- A–C · 560 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–B · 475 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
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 3S5A · PDBe 3S5A · UniProt Q6NS38
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