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Crystal structure of human ALKBH5

Analyse Crystal structure of human ALKBH5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NJ4
Type: protein
Length: 424 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: UN9, MN, NO3
Pockets: 4 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA demethylase ALKBH5 (EC 1.14.11.-)	protein	218	29% helix, 31% strand	Q6P6C2
B	RNA demethylase ALKBH5 (EC 1.14.11.-)	protein	206	27% helix, 32% strand	Q6P6C2

Ligands and binding sites

UN9 · N-[(1-chloro-4-hydroxyisoquinolin-3-yl)carbonyl]glycine · ligand · 2 copies · chains A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B
NO3 · Nitrate ion · ion · 3 copies · chains A, B
GOL · Glycerol · additive · 3 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	870	0.86	0.88	82	UN9, MN, NO3
2	122	0.72	0.92	24	MN, NO3, GOL
3	68	0.32	0.75	17	empty
4	52	0.31	0.77	16	empty

Interfaces

1 interface between chains.

A–B · 849 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 disulfide (covalent ligand, disulfide).

Compared structures

4NJ4 · Crystal Structure of Human ALKBH5 · the same entry in another collection · chain A against A, 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 0.96

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 4NJ4 · PDBe 4NJ4 · UniProt Q6P6C2

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