MolNFT v1 · #170518 · protein
Crystal structure of tswv glycoprotein N ectodomain (trypsin treated)
6YA2: “Crystal structure of tswv glycoprotein N ectodomain (trypsin treated)”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.49). MolNFT v1 #170518 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6YA2
- Type
- protein
- Length
- 551 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein
- UniProt
- A0A3G1GK10
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.49
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein | protein | 188 | 5% helix, 49% strand | A0A3G1GK10 |
| B | Glycoprotein | protein | 190 | 9% helix, 45% strand | A0A3G1GK10 |
| C | Glycoprotein | protein | 173 | 4% helix, 40% strand | A0A3G1GK10 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.49 | 0.74 | 33 | empty |
| 2 | 223 | 0.45 | 0.73 | 26 | empty |
| 3 | 142 | 0.42 | 0.75 | 20 | empty |
| 4 | 114 | 0.38 | 0.74 | 21 | empty |
| 5 | 117 | 0.36 | 0.73 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 983 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 358 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 99 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6YA2 · Crystal structure of TSWV glycoprotein N ectodomain (Trypsin treated) · 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 A0A3G1GK10
- Elsewhere: RCSB PDB 6YA2 · PDBe 6YA2 · UniProt A0A3G1GK10
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.