Research workbench
Structure of rvfv envelope protein gc in postfusion conformation in complex with mes
Analyse Structure of rvfv envelope protein gc in postfusion conformation in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EGT
- Type
- protein
- Length
- 1,334 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein
- UniProt
- A2T087
- Ligands
- NAG, FUL
- Pockets
- 17 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycoprotein | protein | 445 | 4% helix, 57% strand | A2T087 |
| C | Glycoprotein | protein | 444 | 4% helix, 56% strand | A2T087 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, B
- FUL · beta-L-fucopyranose · sugar · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.90 | 0.93 | 110 | empty |
| 2 | 174 | 0.81 | 0.96 | 43 | empty |
| 3 | 326 | 0.76 | 0.87 | 57 | empty |
| 4 | 359 | 0.74 | 0.86 | 60 | empty |
| 5 | 317 | 0.74 | 0.86 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2935 Ų buried · 49 hydrogen bonds · protein-protein
- A–B · 2912 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 2865 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6EGT · Structure of RVFV envelope protein Gc in postfusion conformation in complex with MES · 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 A2T087
- Elsewhere: RCSB PDB 6EGT · PDBe 6EGT · UniProt A2T087
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