Research workbench
JMJD7 in complex with mn and 2OG in the H32 form
Analyse JMJD7 in complex with mn and 2OG in the H32 form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NFN
- Type
- protein
- Length
- 1,270 residues
- Chains
- 4
- 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
- 11 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Jmjc domain-containing protein 7 | protein | 317 | 31% helix, 32% strand | P0C870 |
| B, D | Jmjc domain-containing protein 7 | protein | 318 | 31% helix, 32% strand | P0C870 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 3 copies · chains A, B, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- NO3 · Nitrate ion · ion · 7 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.79 | 0.81 | 110 | MN |
| 2 | 469 | 0.71 | 0.81 | 47 | empty |
| 3 | 62 | 0.69 | 0.96 | 22 | empty |
| 4 | 72 | 0.65 | 0.92 | 23 | empty |
| 5 | 251 | 0.61 | 0.80 | 46 | MN, AKG |
Interfaces
6 interfaces between chains.
- A–B · 1742 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1731 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 661 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 277 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 266 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5NFN · JMJD7 in complex with mn and 2OG in the H32 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 5NFN · PDBe 5NFN · UniProt P0C870
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