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Crystal structure of glycoprotein C from rift valley fever virus (glycosylated)
Analyse Crystal structure of glycoprotein C from rift valley fever virus (glycosylated) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HJ1
- Type
- protein
- Length
- 1,719 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein
- UniProt
- A2T075
- Ligands
- NAG, BMA
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Envelope glycoprotein | protein | 431 | 6% helix, 55% strand | A2T075 |
| B | Envelope glycoprotein | protein | 427 | 6% helix, 52% strand | A2T075 |
| C | Envelope glycoprotein | protein | 430 | 4% helix, 55% strand | A2T075 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 9 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.72 | 0.76 | 105 | empty |
| 2 | 1125 | 0.72 | 0.76 | 97 | empty |
| 3 | 213 | 0.53 | 0.78 | 39 | empty |
| 4 | 196 | 0.53 | 0.78 | 35 | empty |
| 5 | 171 | 0.52 | 0.79 | 30 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1582 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1501 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 76 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4HJ1 · Crystal structure of glycoprotein C from Rift Valley Fever Virus (glycosylated) · 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 A2T075
- Elsewhere: RCSB PDB 4HJ1 · PDBe 4HJ1 · UniProt A2T075
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