MolNFT v1 · #101913 · protein
Structure of human ALKBH5 crystallized in the presence of citrate
4O61 · RNA demethylase ALKBH5: “Structure of human ALKBH5 crystallized in the presence of citrate”. X-ray diffraction, 2 ligands (UNL, UNX), 3 pockets (best druggability 0.78). MolNFT v1 #101913 on GenesisL1: 3D structure, binding sites…
- PDB
- 4O61
- Type
- protein
- Length
- 420 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
- UNL, UNX
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA demethylase ALKBH5 (EC 1.14.11.-) | protein | 211 | 27% helix, 30% strand | Q6P6C2 |
| B | RNA demethylase ALKBH5 (EC 1.14.11.-) | protein | 209 | 27% helix, 30% strand | Q6P6C2 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 30 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.78 | 0.81 | 70 | UNX |
| 2 | 199 | 0.68 | 0.86 | 31 | CIT, UNX |
| 3 | 202 | 0.65 | 0.84 | 32 | CIT, UNX |
Interfaces
1 interface between chains.
- A–B · 650 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
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 4O61 · PDBe 4O61 · UniProt Q6P6C2
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