Research workbench
Drosophila melanogaster JMJD7 (DMJMJD7) in complex with mn and 2OG
Analyse Drosophila melanogaster JMJD7 (DMJMJD7) in complex with mn and 2OG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YXG
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH14974P
- EC
- 1.14.11.-
- UniProt
- Q9VU77
- Ligands
- AKG, MN, MG
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GH14974P (EC 1.14.11.-) | protein | 313 | 28% helix, 35% strand | Q9VU77 |
| B | GH14974P (EC 1.14.11.-) | protein | 312 | 29% helix, 34% strand | Q9VU77 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 74 | 0.73 | 0.97 | 25 | EDO |
| 2 | 204 | 0.61 | 0.82 | 46 | MN, AKG |
| 3 | 148 | 0.60 | 0.84 | 36 | MN, AKG |
| 4 | 112 | 0.52 | 0.82 | 35 | EDO |
| 5 | 90 | 0.38 | 0.77 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1821 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 7YXG · Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and 2OG · the same entry in another collection · 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 Q9VU77
- Elsewhere: RCSB PDB 7YXG · PDBe 7YXG · UniProt Q9VU77
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