MolNFT v1 · #190173 · protein + RNA
Crystal structure of human ALKBH5 in complex with N-oxalylglycine (nog) and M6A-containing ssrna
7WL0 · RNA demethylase ALKBH5: “Crystal structure of human ALKBH5 in complex with N-oxalylglycine (nog) and M6A-containing ssrna”. X-ray diffraction, 2 ligands (OGA, MN), 16 pockets (best druggability 0.79). MolNFT v1 #190173 on GenesisL1…
- PDB
- 7WL0
- Type
- protein + RNA
- Length
- 1,114 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA demethylase ALKBH5; RNA (5'-R(*UP*GP*GP*(6MZ)P*CP*UP*GP*C)-3')
- EC
- 1.14.11.53
- UniProt
- Q6P6C2
- Ligands
- OGA, MN
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA demethylase ALKBH5 (EC 1.14.11.53) | protein | 214 | 24% helix, 31% strand | Q6P6C2 |
| B, F | RNA (5'-R(*UP*GP*GP*(6MZ)P*CP*UP*GP*C)-3') | rna | 8 | — | — |
| C, I | RNA demethylase ALKBH5 (EC 1.14.11.53) | protein | 218 | 25% helix, 30% strand | Q6P6C2 |
| D | RNA (5'-R(*UP*GP*GP*(6MZ)P*CP*UP*GP*C)-3') | rna | 5 | — | — |
| E | RNA demethylase ALKBH5 (EC 1.14.11.53) | protein | 216 | 25% helix, 30% strand | Q6P6C2 |
| G | RNA demethylase ALKBH5 (EC 1.14.11.53) | protein | 219 | 25% helix, 30% strand | Q6P6C2 |
| H, J | RNA (5'-R(*UP*GP*GP*(6MZ)P*CP*UP*GP*C)-3') | rna | 4 | — | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 5 copies · chains A, B, C, D, E, F, G, H, I, J
- MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, D, E, F, G, H, I, J
- FMT · Formic acid · additive · chains C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.79 | 0.81 | 93 | empty |
| 2 | 84 | 0.77 | 0.99 | 24 | MN, OGA |
| 3 | 80 | 0.77 | 0.99 | 24 | MN, OGA |
| 4 | 76 | 0.76 | 0.99 | 24 | MN, OGA |
| 5 | 78 | 0.75 | 0.98 | 24 | MN, OGA |
Interfaces
14 interfaces between chains.
- E–F · 866 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 831 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 816 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 775 Ų buried · 8 hydrogen bonds · protein-nucleic
- G–H · 725 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified (nucleotide modification).
Compared structures
- 7WL0 · Crystal structure of human ALKBH5 in complex with N-oxalylglycine (NOG) and… · the same entry in another collection · chain G against G, 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 0.99
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 7WL0 · PDBe 7WL0 · UniProt Q6P6C2
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