Research workbench
Structure of gc glycoprotein from severe fever with thrombocytopenia syndrome virus in the trimeric postfusion conformation
Analyse Structure of gc glycoprotein from severe fever with thrombocytopenia syndrome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G47
- Type
- protein
- Length
- 1,284 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sftsv gc
- UniProt
- R4V2Q5
- Ligands
- NAG, CL
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Sftsv gc | protein | 428 | 6% helix, 54% strand | R4V2Q5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.84 | 0.86 | 89 | empty |
| 2 | 358 | 0.82 | 0.91 | 61 | empty |
| 3 | 141 | 0.81 | 0.98 | 26 | empty |
| 4 | 503 | 0.80 | 0.87 | 68 | empty |
| 5 | 501 | 0.79 | 0.86 | 64 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2609 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2600 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 2516 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 3 glycan (disulfide, N-glycosylation).
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 R4V2Q5
- Elsewhere: RCSB PDB 5G47 · PDBe 5G47 · UniProt R4V2Q5
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