Research workbench
Crystal structure of human ALKBH5 crystallized in the presence of MN^{2+} and 2-oxoglutarate
Analyse Crystal structure of human ALKBH5 crystallized in the presence of MN^{2+} and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OCT
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA demethylase ALKBH5
- EC
- 1.14.11.-
- UniProt
- Q6P6C2
- Ligands
- AKG, MN, UNX
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA demethylase ALKBH5 (EC 1.14.11.-) | protein | 209 | 26% helix, 30% strand | Q6P6C2 |
| B | RNA demethylase ALKBH5 (EC 1.14.11.-) | protein | 210 | 27% helix, 30% strand | Q6P6C2 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 23 copies · chains A, B
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 | 762 | 0.77 | 0.81 | 58 | UNX |
| 2 | 172 | 0.66 | 0.86 | 31 | MN, AKG, UNX |
| 3 | 181 | 0.65 | 0.85 | 36 | MN, AKG, UNX |
| 4 | 64 | 0.30 | 0.74 | 13 | UNX |
Interfaces
1 interface between chains.
- A–B · 612 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4OCT · Crystal structure of human ALKBH5 crystallized in the presence of Mn^{2+} and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6P6C2 · AlphaFold monomer V2.0 prediction for RNA demethylase ALKBH5 (Q6P6C2) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q6P6C2
- Elsewhere: RCSB PDB 4OCT · PDBe 4OCT · UniProt Q6P6C2
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