Research workbench
Rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122
Analyse Rabies virus glycoprotein pre-fusion trimer in complex with neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U9G
- Type
- protein
- Length
- 1,860 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein; RVA122 Fab light chain; RVA122 Fab heavy chain
- UniProt
- P08667
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Glycoprotein | protein | 389 | 19% helix, 35% strand | P08667 |
| D, E, F | RVA122 Fab light chain | protein | 109 | 3% helix, 44% strand | — |
| G, H, I | RVA122 Fab heavy chain | protein | 122 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1102 | 0.82 | 0.83 | 97 | empty |
| 2 | 1072 | 0.82 | 0.83 | 102 | empty |
| 3 | 312 | 0.77 | 0.88 | 46 | empty |
| 4 | 624 | 0.77 | 0.83 | 58 | empty |
| 5 | 331 | 0.76 | 0.87 | 53 | empty |
Interfaces
18 interfaces between chains.
- A–C · 932 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 924 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 916 Ų buried · 12 hydrogen bonds · protein-protein
- B–G · 891 Ų buried · 7 hydrogen bonds · protein-protein
- C–H · 883 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 7U9G · Rabies virus glycoprotein pre-fusion trimer in complex with neutralizing antibody RVA122 · the same entry in another collection · chain F against F, 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 P08667
- Elsewhere: RCSB PDB 7U9G · PDBe 7U9G · UniProt P08667
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