Human JMJD5 (N308C) in complex with Mn(II), 2OG and RCCD1 (139-143) (complex-4)

Structure

x-ray diffraction · resolution 1.461 · 2 distinct chains · 26% helix, 33% strand (DSSP).

Ligands and binding sites

• AKG · 2-oxoglutaric acid · ligand · chains A, B
• MN · Manganese (II) ion · metal · chains A
• TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
• GOL · Glycerol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

• A–B · 463 Ų buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

• 6F4S · Human JMJD5 (N308C) in complex with MN(II), 2OG and RCCD1 (139-143) (complex-4) · the same entry in another collection · chain A against A, TM-score 1.00
• Q8N371 · AlphaFold monomer V2.0 prediction for bifunctional peptidase and arginyl-hydroxylase… · a predicted model of the same protein · chain A against A, TM-score 1.00
• A6NED2 · AlphaFold monomer V2.0 prediction for RCC1 domain-containing protein 1 (A6NED2) · a predicted model of the same protein · chain B against A, TM-score 0.57

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 Q8N371
• Every structure of UniProt A6NED2
• Elsewhere: RCSB PDB 6F4S · PDBe 6F4S · UniProt Q8N371 · UniProt A6NED2