Research workbench
Rift valley fever virus gn in complex with a neutralizing antibody fragment
Analyse Rift valley fever virus gn in complex with a neutralizing antibody fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I9I
- Type
- protein
- Length
- 955 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rv-GN1 heavy chain; Rv-GN1 light chain; Glycoprotein
- UniProt
- A2T080
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rv-GN1 heavy chain | protein | 208 | 4% helix, 50% strand | — |
| B | Rv-GN1 light chain | protein | 216 | 6% helix, 52% strand | — |
| C | Glycoprotein | protein | 52 | 17% helix, 29% strand | A2T080 |
| D | Glycoprotein | protein | 51 | 18% helix, 29% strand | A2T080 |
| H | Rv-GN1 heavy chain | protein | 213 | 4% helix, 49% strand | — |
| L | Rv-GN1 light chain | protein | 215 | 6% helix, 53% strand | — |
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 919 | 0.78 | 0.80 | 77 | empty |
| 2 | 321 | 0.60 | 0.77 | 41 | empty |
| 3 | 145 | 0.51 | 0.80 | 30 | empty |
| 4 | 76 | 0.46 | 0.82 | 27 | empty |
| 5 | 95 | 0.37 | 0.75 | 29 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1873 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 1866 Ų buried · 20 hydrogen bonds · protein-protein
- D–H · 641 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 637 Ų buried · 12 hydrogen bonds · protein-protein
- D–L · 302 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 6I9I · Rift valley fever virus Gn in complex with a neutralizing antibody fragment · 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 A2T080
- Elsewhere: RCSB PDB 6I9I · PDBe 6I9I · UniProt A2T080
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