Research workbench
JmjC domain-containing protein 5 (JMJD5) in complex with Mn and pyridine-2,4-dicarboxylic acid (2,4-PDCA)
Analyse JmjC domain-containing protein 5 (JMJD5) in complex with Mn and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I9L
- Type
- protein
- Length
- 228 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.53
- Source
- Homo sapiens
- Molecule
- JmjC domain-containing protein 5
- EC
- 1.14.11.27, 3.4.-.-
- UniProt
- Q8N371
- Ligands
- PD2, MN
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · resolution 1.53 · 1 distinct chain · 26% 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 | 26% helix, 34% strand | Q8N371 |
Ligands and binding sites
- PD2 · Pyridine-2,4-dicarboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 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 | 145 | 0.51 | 0.79 | 28 | MN, PD2 |
Compared structures
- 6I9L · Jmjc domain-containing protein 5 (JMJD5) in complex with mn and pyridine-2,4-dicarboxylic… · 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 6I9L · PDBe 6I9L · UniProt Q8N371
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.