MolNFT v1 · #147552 · protein
Structure of rvfv envelope protein gc in postfusion conformation in complex with 1,2-dipropionyl-sn-glycero-3-phosphocholine
6EGU: “Structure of rvfv envelope protein gc in postfusion conformation in complex with…”. X-ray diffraction, 3 ligands (43Y, NAG, FUL), 18 pockets (best druggability 0.88). MolNFT v1 #147552 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6EGU
- Type
- protein
- Length
- 1,327 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rvfv envelope protein gc
- UniProt
- A2T087
- Ligands
- 43Y, NAG, FUL
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rvfv envelope protein gc | protein | 443 | 4% helix, 57% strand | A2T087 |
| B | Rvfv envelope protein gc | protein | 440 | 4% helix, 58% strand | A2T087 |
| C | Rvfv envelope protein gc | protein | 444 | 4% helix, 56% strand | A2T087 |
Ligands and binding sites
- 43Y · [(2R)-3-[oxidanyl-[2-(trimethyl-$L^{4}-azanyl) ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, B
- FUL · beta-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 846 | 0.88 | 0.91 | 110 | empty |
| 2 | 122 | 0.77 | 0.96 | 30 | empty |
| 3 | 326 | 0.72 | 0.85 | 45 | empty |
| 4 | 380 | 0.72 | 0.83 | 49 | empty |
| 5 | 243 | 0.71 | 0.87 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–C · 3014 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2973 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 2963 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6EGU · Structure of RVFV envelope protein Gc in postfusion conformation in complex with… · 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 6EGU · PDBe 6EGU · UniProt A2T087
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