Research workbench
Drosophila melanogaster JMJD7 (DMJMJD7) in complex with mn and 2,4- pdca
Analyse Drosophila melanogaster JMJD7 (DMJMJD7) in complex with mn and 2,4- pdca in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YXJ
- Type
- protein
- Length
- 1,238 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GH14974P
- EC
- 1.14.11.-
- UniProt
- Q9VU77
- Ligands
- PD2, MN
- Pockets
- 17 · best druggability 0.69
Structure
x-ray diffraction · 4 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 | 309 | 27% helix, 37% strand | Q9VU77 |
| C | GH14974P (EC 1.14.11.-) | protein | 309 | 27% helix, 37% strand | Q9VU77 |
| D | GH14974P (EC 1.14.11.-) | protein | 308 | 28% helix, 36% strand | Q9VU77 |
Ligands and binding sites
- PD2 · Pyridine-2,4-dicarboxylic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.69 | 0.85 | 35 | MN, EDO, PD2 |
| 2 | 200 | 0.66 | 0.85 | 37 | MN, EDO, PD2 |
| 3 | 148 | 0.63 | 0.86 | 40 | EDO |
| 4 | 155 | 0.63 | 0.85 | 36 | EDO |
| 5 | 195 | 0.61 | 0.82 | 41 | MN, PD2 |
Interfaces
3 interfaces between chains.
- C–D · 1854 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1848 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 7YXJ · Drosophila melanogaster JMJD7 (dmJMJD7) in complex with Mn and 2,4-PDCA · 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 7YXJ · PDBe 7YXJ · UniProt Q9VU77
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