MolNFT v1 · #190781 · protein
Drosophila melanogaster JMJD7 (DMJMJD7) in complex with mn and succinate
7YXH · GH14974P: “Drosophila melanogaster JMJD7 (DMJMJD7) in complex with mn and succinate”. X-ray diffraction, 2 ligands (MN, MG), 9 pockets (best druggability 0.71). MolNFT v1 #190781 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7YXH
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH14974P
- EC
- 1.14.11.-
- UniProt
- Q9VU77
- Ligands
- MN, MG
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 36% 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 | 301 | 27% helix, 37% strand | Q9VU77 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.71 | 0.96 | 22 | empty |
| 2 | 250 | 0.68 | 0.84 | 36 | empty |
| 3 | 144 | 0.63 | 0.86 | 39 | empty |
| 4 | 224 | 0.63 | 0.82 | 42 | MN, SIN |
| 5 | 189 | 0.51 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1819 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7YXH · Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and succinate · 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 7YXH · PDBe 7YXH · UniProt Q9VU77
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