MolNFT v1 · #170501 · protein
Crystal structure of tswv glycoprotein N ectodomain (sgn)
6Y9L: “Crystal structure of tswv glycoprotein N ectodomain (sgn)”. X-ray diffraction, 2 ligands (NAG, BMA), 14 pockets (best druggability 0.70). MolNFT v1 #170501 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Y9L
- Type
- protein
- Length
- 783 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein
- UniProt
- A0A3G1GK10
- Ligands
- NAG, BMA
- Pockets
- 14 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Glycoprotein | protein | 196 | 7% helix, 36% strand | A0A3G1GK10 |
| D | Glycoprotein | protein | 196 | 9% helix, 39% strand | A0A3G1GK10 |
| A | Glycoprotein | protein | 197 | 7% helix, 41% strand | A0A3G1GK10 |
| C | Glycoprotein | protein | 194 | 5% helix, 39% strand | A0A3G1GK10 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains B, D, A, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 429 | 0.70 | 0.81 | 48 | empty |
| 2 | 182 | 0.67 | 0.86 | 28 | empty |
| 3 | 500 | 0.63 | 0.76 | 63 | empty |
| 4 | 187 | 0.63 | 0.83 | 30 | empty |
| 5 | 393 | 0.57 | 0.75 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–C · 986 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 942 Ų buried · 10 hydrogen bonds · protein-protein
- D–C · 764 Ų buried · 8 hydrogen bonds · protein-protein
- B–A · 685 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6Y9L · Crystal structure of TSWV glycoprotein N ectodomain (sGn) · the same entry in another collection · chain B against B, 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 6Y9L · PDBe 6Y9L · UniProt A0A3G1GK10
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