Research workbench
Crystal structure of mouse JMJD7 fused with maltose-binding protein
Analyse Crystal structure of mouse JMJD7 fused with maltose-binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QSZ
- Type
- protein
- Length
- 1,368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein, jmjc domain-containing protein 7 chimera
- UniProt
- P0AEX9, P0C872
- Ligands
- GLC
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein, jmjc domain-containing protein 7 chimera | protein | 686 | 36% helix, 24% strand | P0AEX9, P0C872 |
| B | Maltose-binding periplasmic protein, jmjc domain-containing protein 7 chimera | protein | 682 | 35% helix, 25% strand | P0AEX9, P0C872 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- FLC · Citrate anion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.80 | 0.85 | 68 | empty |
| 2 | 1043 | 0.79 | 0.80 | 95 | empty |
| 3 | 323 | 0.76 | 0.87 | 27 | GLC, FLC |
| 4 | 405 | 0.74 | 0.84 | 28 | GLC, FLC |
| 5 | 191 | 0.60 | 0.82 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 2785 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4QSZ · Crystal structure of mouse JMJd7 fused with maltose-binding protein · the same entry in another collection · chain A against A, TM-score 1.00
- P0C872 · AlphaFold monomer V2.0 prediction for bifunctional peptidase and (3S)-lysyl hydroxylase… · a predicted model of the same protein · chain B against A, TM-score 0.46
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 P0AEX9
- Every structure of UniProt P0C872
- Elsewhere: RCSB PDB 4QSZ · PDBe 4QSZ · UniProt P0AEX9 · UniProt P0C872
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