Research workbench
Crystal structure of the paralogue of the human formylglycine generating enzyme
Analyse Crystal structure of the paralogue of the human formylglycine generating enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y4J
- Type
- protein
- Length
- 534 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfatase modifying factor 2
- UniProt
- Q8NBJ7
- Ligands
- NAG, FUC, CA
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfatase modifying factor 2 | protein | 266 | 17% helix, 22% strand | Q8NBJ7 |
| B | Sulfatase modifying factor 2 | protein | 268 | 19% helix, 22% strand | Q8NBJ7 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar
- CA · Calcium ion · metal · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.81 | 0.82 | 70 | MPD |
| 2 | 326 | 0.66 | 0.81 | 34 | empty |
| 3 | 107 | 0.45 | 0.79 | 20 | empty |
| 4 | 83 | 0.41 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1188 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1Y4J · Crystal structure of the paralogue of the human formylglycine generating enzyme · the same entry in another collection · chain A against A, TM-score 1.00
- Q8NBJ7 · AlphaFold monomer V2.0 prediction for inactive C-alpha-formylglycine- generating enzyme 2… · a predicted model of the same protein · chain B 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 Q8NBJ7
- Elsewhere: RCSB PDB 1Y4J · PDBe 1Y4J · UniProt Q8NBJ7
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