MolNFT v1 · #152315 · protein
Peptide asparaginyl ligases from viola yedoensis
6IDV: “Peptide asparaginyl ligases from viola yedoensis”. X-ray diffraction, 3 ligands (SNN, NAG, FUC), 6 pockets (best druggability 0.62). MolNFT v1 #152315 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IDV
- Type
- protein
- Length
- 850 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide asparaginyl ligases
- Ligands
- SNN, NAG, FUC
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide asparaginyl ligases | protein | 425 | 44% helix, 11% strand | — |
| B | Peptide asparaginyl ligases | protein | 425 | 44% helix, 11% strand | — |
Ligands and binding sites
- SNN · L-3-aminosuccinimide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.62 | 0.93 | 25 | empty |
| 2 | 270 | 0.61 | 0.80 | 37 | SNN |
| 3 | 300 | 0.59 | 0.78 | 41 | empty |
| 4 | 184 | 0.53 | 0.79 | 41 | empty |
| 5 | 165 | 0.50 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 893 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 disulfide, 4 glycan (covalent ligand, disulfide, N-glycosylation).
Compared structures
- 6IDV · Peptide Asparaginyl Ligases from Viola yedoensis · 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
- Elsewhere: RCSB PDB 6IDV · PDBe 6IDV
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