MolNFT v1 · #92810 · protein
JMJD5 in complex with 2-oxoglutarate
4GJZ · Jmjc domain-containing protein 5: “JMJD5 in complex with 2-oxoglutarate”. X-ray diffraction, 2 ligands (AKG, CO), 1 pocket (best druggability 0.51). MolNFT v1 #92810 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GJZ
- 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
- UniProt
- Q8N371
- Ligands
- AKG, CO
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing protein 5 (EC 1.14.11.27) | protein | 228 | 25% helix, 34% strand | Q8N371 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- CO · Cobalt (II) ion · metal · chains A
- BME · Beta-mercaptoethanol · 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 | 162 | 0.51 | 0.79 | 34 | CO, AKG |
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
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 4GJZ · PDBe 4GJZ · UniProt Q8N371
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