MolNFT v1 · #147551 · protein
Structure of rvfv envelope protein gc in postfusion conformation in complex with mes
6EGT · Glycoprotein: “Structure of rvfv envelope protein gc in postfusion conformation in complex with mes”. X-ray diffraction, 2 ligands (NAG, FUL), 17 pockets (best druggability 0.90). MolNFT v1 #147551 on GenesisL1: 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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