Research workbench
Human JMJD5 in complex with MN and 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid.
Analyse Human JMJD5 in complex with MN and 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DYW
- Type
- protein
- Length
- 236 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.13
- Source
- Homo sapiens
- Molecule
- Bifunctional peptidase and arginyl-hydroxylase JMJD5
- EC
- 1.14.11.-, 3.4.-.-
- UniProt
- Q8N371
- Ligands
- HRL, MN
- Pockets
- 1 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.13 · 1 distinct chain · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional peptidase and arginyl-hydroxylase JMJD5 (EC 1.14.11.-, 3.4.-.-) | protein | 236 | 25% helix, 33% strand | Q8N371 |
Ligands and binding sites
- HRL · 5-((2-methoxybenzyl)amino)pyridine-2,4-dicarboxylic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 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 | 399 | 0.64 | 0.78 | 42 | HRL, MN |
Compared structures
- 7DYW · Human JMJD5 in complex with mn and 5-((2-METHOXYBENZYL)AMINO)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 0.98
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 7DYW · PDBe 7DYW · UniProt Q8N371
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