Research workbench
Model of the rift valley fever virus glycoprotein hexamer type 1
Analyse Model of the rift valley fever virus glycoprotein hexamer type 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F9C
- Type
- protein
- Length
- 4,392 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein
- UniProt
- A2T085, A2T072
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 7% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Glycoprotein | protein | 301 | 12% helix, 19% strand | A2T085 |
| B, D, F, H, J, L | Glycoprotein | protein | 431 | 3% helix, 45% strand | A2T072 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 845 | 0.82 | 0.85 | 90 | empty |
| 2 | 1160 | 0.81 | 0.82 | 118 | empty |
| 3 | 1085 | 0.80 | 0.82 | 91 | empty |
| 4 | 1032 | 0.80 | 0.82 | 82 | empty |
| 5 | 561 | 0.78 | 0.84 | 52 | empty |
Interfaces
29 interfaces between chains.
- E–F · 1036 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1031 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1017 Ų buried · 8 hydrogen bonds · protein-protein
- H–J · 1007 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 954 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6F9C · Model of the Rift Valley fever virus glycoprotein hexamer type 1 · 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 A2T085
- Every structure of UniProt A2T072
- Elsewhere: RCSB PDB 6F9C · PDBe 6F9C · UniProt A2T085 · UniProt A2T072
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