MolNFT v1 · #176826 · protein
Human JMJD5 in complex with mn and 5-((4-PHENYLBUTYL)AMINO)PYRIDINE-2, 4-dicarboxylic acid.
7DYU · Bifunctional peptidase and arginyl-hydroxylase JMJD5: “Human JMJD5 in complex with mn and 5-((4-PHENYLBUTYL)AMINO)PYRIDINE-2, 4-dicarboxylic acid.”. X-ray diffraction, 2 ligands (HR9, MN), 1 pocket (best druggability 0.58). MolNFT…
- PDB
- 7DYU
- Type
- protein
- Length
- 228 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional peptidase and arginyl-hydroxylase JMJD5
- EC
- 1.14.11.-, 3.4.-.-
- UniProt
- Q8N371
- Ligands
- HR9, MN
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 28% 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 | 228 | 28% helix, 33% strand | Q8N371 |
Ligands and binding sites
- HR9 · 5-(4-phenylbutylamino)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 · 2 copies · 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 | 226 | 0.58 | 0.79 | 29 | MN, HR9 |
Compared structures
- 7DYU · Human JMJD5 in complex with MN and 5-((4-phenylbutyl)amino)pyridine-2,4-dicarboxylic acid. · 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 7DYU · PDBe 7DYU · UniProt Q8N371
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.