Research workbench
Crystal structure of human ALKBH5 in complex with M6A-containing ssrna
Analyse Crystal structure of human ALKBH5 in complex with M6A-containing ssrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V4G
- Type
- protein + RNA
- Length
- 652 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(P*GP*GP*(6MZ)P*C)-3'); RNA demethylase ALKBH5
- EC
- 1.14.11.53
- UniProt
- Q6P6C2
- Ligands
- MN, SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, E, F | RNA (5'-R(P*GP*GP*(6MZ)P*C)-3') | rna | 4 | — | — |
| A | RNA demethylase ALKBH5 (EC 1.14.11.53) | protein | 212 | 25% helix, 33% strand | Q6P6C2 |
| B, C | RNA demethylase ALKBH5 (EC 1.14.11.53) | protein | 214 | 25% helix, 31% strand | Q6P6C2 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains D, A, E, B, F, C
- SO4 · Sulfate ion · ion · 3 copies · chains D, A, E, B, F, C
- GOL · Glycerol · additive · 4 copies · chains D, E, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.77 | 0.99 | 24 | MN, SO4 |
| 2 | 80 | 0.77 | 0.99 | 23 | MN, SO4 |
| 3 | 63 | 0.75 | 0.99 | 22 | MN, SO4 |
| 4 | 722 | 0.66 | 0.75 | 70 | empty |
| 5 | 315 | 0.58 | 0.77 | 33 | empty |
Interfaces
7 interfaces between chains.
- E–B · 778 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–A · 761 Ų buried · 14 hydrogen bonds · protein-nucleic
- F–C · 757 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 326 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 241 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 7V4G · Crystal structure of human ALKBH5 in complex with m6A-containing ssRNA · the same entry in another collection · chain C against C, TM-score 1.00
- Q6P6C2 · AlphaFold monomer V2.0 prediction for RNA demethylase ALKBH5 (Q6P6C2) · a predicted model of the same protein · chain B 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 7V4G · PDBe 7V4G · UniProt Q6P6C2
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