Research workbench
Human JMJD7 in complex with mn and 2OG in the P21212 form
Analyse Human JMJD7 in complex with mn and 2OG in the P21212 form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NFO
- Type
- protein
- Length
- 635 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing protein 7
- UniProt
- P0C870
- Ligands
- AKG, MN, NO3
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing protein 7 | protein | 317 | 31% helix, 32% strand | P0C870 |
| B | Jmjc domain-containing protein 7 | protein | 318 | 31% helix, 32% strand | P0C870 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.62 | 0.88 | 27 | empty |
| 2 | 184 | 0.60 | 0.82 | 34 | MN, AKG, GOL |
| 3 | 108 | 0.58 | 0.85 | 29 | GOL |
| 4 | 181 | 0.58 | 0.81 | 31 | MN, AKG |
Interfaces
1 interface between chains.
- A–B · 1754 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5NFO · Human JMJD7 in complex with Mn and 2OG in the P21212 form · the same entry in another collection · chain A against A, TM-score 1.00
- P0C870 · AlphaFold monomer V2.0 prediction for bifunctional peptidase and (3S)-lysyl hydroxylase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0C870
- Elsewhere: RCSB PDB 5NFO · PDBe 5NFO · UniProt P0C870
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