Research workbench
Asymmetric unit of rift valley fever virus glycoprotein shell
Analyse Asymmetric unit of rift valley fever virus glycoprotein shell in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F9B
- Type
- protein
- Length
- 8,784 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein
- UniProt
- A2T085, A2T072
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 7% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, X | Glycoprotein | protein | 301 | 10% helix, 29% strand | A2T085 |
| B, D, F, H, J, L, N, P, R, T, V, Y | Glycoprotein | protein | 431 | 4% helix, 43% 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 | 1105 | 0.84 | 0.85 | 135 | empty |
| 2 | 906 | 0.83 | 0.85 | 90 | empty |
| 3 | 1084 | 0.81 | 0.82 | 82 | empty |
| 4 | 985 | 0.81 | 0.82 | 83 | empty |
| 5 | 757 | 0.79 | 0.83 | 63 | empty |
Interfaces
51 interfaces between chains.
- S–T · 1301 Ų buried · 15 hydrogen bonds · protein-protein
- V–Y · 1158 Ų buried · 11 hydrogen bonds · protein-protein
- Q–R · 1135 Ų buried · 6 hydrogen bonds · protein-protein
- X–Y · 1106 Ų buried · 11 hydrogen bonds · protein-protein
- U–V · 1091 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 252 disulfide (disulfide).
Compared structures
- 6F9B · Asymmetric unit of Rift Valley fever virus glycoprotein shell · 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 6F9B · PDBe 6F9B · UniProt A2T085 · UniProt A2T072
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