MolNFT v1 · #154973 · protein + DNA
Crystal structure of ALKBH1 bound to 21-mer DNA bulge
6KSF · Alpha-ketoglutarate-dependent dioxygenase alkb homolog 1: “Crystal structure of ALKBH1 bound to 21-mer DNA bulge”. X-ray diffraction, 2 ligands (XL3, CL), 6 pockets (best druggability 0.78). MolNFT v1 #154973 on GenesisL1: 3D…
- PDB
- 6KSF
- Type
- protein + DNA
- Length
- 380 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent dioxygenase alkb homolog 1; DNA (5'…
- Ligands
- XL3, CL
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent dioxygenase alkb homolog 1 | protein | 335 | 27% helix, 23% strand | — |
| B | DNA (5'- D(*DGP*DCP*DTP*DGP*DAP*DGP*DTP*DGP*DCP*DCP*DCP*DGP*DCP*DGP*DTP*DGP*DC P*DTP*DGP*DGP*DAP*DTP*DCP*DC)-3') | dna | 24 | — | — |
| C | DNA (5'- D(*DGP*DGP*DAP*DTP*DCP*DCP*DAP*DGP*DCP*DAP*DCP*DGP*DCP*DCP*DAP*DCP*DT P*DCP*DAP*DGP*DC)-3') | dna | 21 | — | — |
Ligands and binding sites
- XL3 · propane-1-thiol · ligand · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A
- SIN · Succinic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.78 | 0.80 | 76 | SIN, XL3 |
| 2 | 228 | 0.53 | 0.77 | 34 | empty |
| 3 | 129 | 0.39 | 0.74 | 29 | empty |
| 4 | 52 | 0.36 | 0.79 | 17 | empty |
| 5 | 73 | 0.31 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1061 Ų buried · 102 hydrogen bonds · nucleic-nucleic
- A–B · 740 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 367 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6KSF · Crystal Structure of ALKBH1 bound to 21-mer DNA bulge · the same entry in another collection · 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
- Elsewhere: RCSB PDB 6KSF · PDBe 6KSF
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