MolNFT v1 · #178132 · protein
A mutant of an enzyme from viola yedoensis
7F5J · Peptide asparaginyl ligases: “A mutant of an enzyme from viola yedoensis”. X-ray diffraction, 2 ligands (NAG, FUC), 1 pocket (best druggability 0.62). MolNFT v1 #178132 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7F5J
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide asparaginyl ligases
- UniProt
- A0A509GV09
- Ligands
- NAG, FUC
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide asparaginyl ligases | protein | 275 | 33% helix, 17% strand | A0A509GV09 |
| B | Peptide asparaginyl ligases | protein | 271 | 33% helix, 17% strand | A0A509GV09 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.62 | 0.77 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 369 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide, 2 modified (N-glycosylation, disulfide, nonstandard).
Compared structures
- 7F5J · The crystal structure of VyPAL2-I244V, a more efficient mutant of VyPAL2 peptide… · 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 A0A509GV09
- Elsewhere: RCSB PDB 7F5J · PDBe 7F5J · UniProt A0A509GV09
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