Research workbench
Crystal structure of human ALKBH5 in complex with 2-oxoglutarate (2OG) and M6A-containing ssrna
Analyse Crystal structure of human ALKBH5 in complex with 2-oxoglutarate (2OG) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WKV
- Type
- protein + RNA
- Length
- 669 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA demethylase ALKBH5; RNA (5'-R(P*GP*GP*(6MZ)P*C)-3')
- EC
- 1.14.11.53
- UniProt
- Q6P6C2
- Ligands
- AKG, MN
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | RNA demethylase ALKBH5 (EC 1.14.11.53) | protein | 219 | 26% helix, 33% strand | Q6P6C2 |
| B, D, F | RNA (5'-R(P*GP*GP*(6MZ)P*C)-3') | rna | 4 | — | — |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, C, D, E, F
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.78 | 0.99 | 24 | MN, AKG |
| 2 | 85 | 0.77 | 0.99 | 23 | AKG |
| 3 | 81 | 0.77 | 0.99 | 23 | AKG |
| 4 | 1083 | 0.72 | 0.76 | 93 | empty |
Interfaces
8 interfaces between chains.
- A–B · 781 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–D · 734 Ų buried · 14 hydrogen bonds · protein-nucleic
- E–F · 708 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–E · 237 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 148 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 7WKV · Crystal structure of human ALKBH5 in complex with 2-oxoglutarate (2OG) and m6A-containing… · the same entry in another collection · chain F against F, TM-score 1.00
- Q6P6C2 · AlphaFold monomer V2.0 prediction for RNA demethylase ALKBH5 (Q6P6C2) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 7WKV · PDBe 7WKV · UniProt Q6P6C2
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