Research workbench
Junin virus GP1 glycoprotein in complex with Fab fragment of antibody JUN1
Analyse Junin virus GP1 glycoprotein in complex with Fab fragment of antibody JUN1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QU2
- Type
- protein
- Length
- 586 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab JUN1 heavy chain; Fab JUN1 light chain; Glycoprotein G1
- UniProt
- C1K9J9
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab JUN1 heavy chain | protein | 230 | 5% helix, 48% strand | — |
| B | Fab JUN1 light chain | protein | 214 | 7% helix, 50% strand | — |
| C | Glycoprotein G1 | protein | 142 | 26% helix, 25% strand | C1K9J9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C
- GOL · Glycerol · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.56 | 0.80 | 23 | empty |
| 2 | 159 | 0.53 | 0.80 | 26 | empty |
| 3 | 189 | 0.47 | 0.75 | 23 | empty |
| 4 | 90 | 0.46 | 0.81 | 28 | GOL |
| 5 | 112 | 0.41 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1978 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 445 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7QU2 · Junin virus GP1 glycoprotein in complex with Fab fragment of antibody JUN1 · 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 C1K9J9
- Elsewhere: RCSB PDB 7QU2 · PDBe 7QU2 · UniProt C1K9J9
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