Research workbench
Jmjc domain-containing protein 5 (JMJD5) in complex with mn and R-2- hydroxyglutarate
Analyse Jmjc domain-containing protein 5 (JMJD5) in complex with mn and R-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I9M
- Type
- protein
- Length
- 228 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing protein 5
- EC
- 1.14.11.27, 3.4.-.-
- UniProt
- Q8N371
- Ligands
- 2HG, MN
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing protein 5 (EC 1.14.11.27, 3.4.-.-) | protein | 228 | 27% helix, 34% strand | Q8N371 |
Ligands and binding sites
- 2HG · (2R)-2-hydroxypentanedioic acid · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.52 | 0.79 | 31 | MN, 2HG, GOL |
Compared structures
- 6I9M · JmjC domain-containing protein 5 (JMJD5) in complex with Mn and R-2-hydroxyglutarate · 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
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
- Elsewhere: RCSB PDB 6I9M · PDBe 6I9M · UniProt Q8N371
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