Research workbench
Drosophila melanogaster JMJD7 (DMJMJD7) in complex with mn and N- oxalylglycine (nog)
Analyse Drosophila melanogaster JMJD7 (DMJMJD7) in complex with mn and N- oxalylglycine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YXI
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH14974P
- EC
- 1.14.11.-
- UniProt
- Q9VU77
- Ligands
- OGA, MN, SO4
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GH14974P (EC 1.14.11.-) | protein | 312 | 29% helix, 35% strand | Q9VU77 |
| B | GH14974P (EC 1.14.11.-) | protein | 312 | 29% helix, 35% strand | Q9VU77 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.73 | 0.96 | 23 | empty |
| 2 | 149 | 0.64 | 0.86 | 43 | SO4 |
| 3 | 240 | 0.62 | 0.81 | 41 | OGA, EDO |
| 4 | 172 | 0.57 | 0.81 | 35 | MN, OGA |
| 5 | 84 | 0.40 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1800 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 7YXI · Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and N-oxalylglycine (NOG) · 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 7YXI · PDBe 7YXI · UniProt Q9VU77
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