MolNFT v1 · #101386 · protein
Crystal structure of zebrafish ALKBH5 in complex with succinic acid
4NPM · RNA demethylase ALKBH5: “Crystal structure of zebrafish ALKBH5 in complex with succinic acid”. X-ray diffraction, 1 ligand (MN), 4 pockets (best druggability 0.68). MolNFT v1 #101386 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4NPM
- Type
- protein
- Length
- 414 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA demethylase ALKBH5
- EC
- 1.14.11.-
- UniProt
- Q08BA6
- Ligands
- MN
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA demethylase ALKBH5 (EC 1.14.11.-) | protein | 210 | 26% helix, 31% strand | Q08BA6 |
| B | RNA demethylase ALKBH5 (EC 1.14.11.-) | protein | 204 | 25% helix, 33% strand | Q08BA6 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SIN · Succinic acid · additive · 2 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 | 150 | 0.68 | 0.88 | 34 | MN, SIN |
| 2 | 135 | 0.67 | 0.89 | 28 | MN, SIN |
| 3 | 258 | 0.57 | 0.78 | 37 | empty |
| 4 | 53 | 0.25 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 277 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4NPM · Crystal structure of Zebrafish ALKBH5 in complex with succinic acid · the same entry in another collection · chain A against A, TM-score 1.00
- Q08BA6 · AlphaFold monomer V2.0 prediction for RNA demethylase ALKBH5 (Q08BA6) · 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 Q08BA6
- Elsewhere: RCSB PDB 4NPM · PDBe 4NPM · UniProt Q08BA6
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