Research workbench
Crystal structure of a jumonji domain-containing protein JMJD5
Analyse Crystal structure of a jumonji domain-containing protein JMJD5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GAZ
- Type
- protein
- Length
- 470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 8
- EC
- 1.14.11.27
- UniProt
- Q8N371
- Ligands
- OGA, NI
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lysine-specific demethylase 8 (EC 1.14.11.27) | protein | 235 | 25% helix, 33% strand | Q8N371 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.61 | 0.85 | 27 | NI, OGA |
| 2 | 108 | 0.60 | 0.87 | 21 | NI, OGA |
| 3 | 257 | 0.49 | 0.74 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 131 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4GAZ · Crystal Structure of a Jumonji Domain-containing Protein JMJD5 · 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 4GAZ · PDBe 4GAZ · UniProt Q8N371
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