Research workbench
Crystal structure of tswv glycoprotein N ectodomain (trypsin treated)
Analyse Crystal structure of tswv glycoprotein N ectodomain (trypsin treated) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YA0
- Type
- protein
- Length
- 553 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein
- UniProt
- A0A3G1GK10
- Ligands
- NAG, BMA, NH4
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoprotein | protein | 190 | 10% helix, 42% strand | A0A3G1GK10 |
| B | Glycoprotein | protein | 189 | 7% helix, 46% strand | A0A3G1GK10 |
| C | Glycoprotein | protein | 174 | 7% helix, 37% strand | A0A3G1GK10 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C, A, B
- BMA · beta-D-mannopyranose · sugar
- NH4 · Ammonium ion · ion · chains C
- ACT · Acetate ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.59 | 0.75 | 58 | empty |
| 2 | 140 | 0.44 | 0.76 | 33 | NH4 |
| 3 | 95 | 0.32 | 0.73 | 20 | empty |
| 4 | 66 | 0.32 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 990 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 685 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6YA0 · 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 6YA0 · PDBe 6YA0 · UniProt A0A3G1GK10
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