Research workbench
Junin virus GP1 glycoprotein in complex with an antibody Fab fragment
Analyse Junin virus GP1 glycoprotein in complex with an antibody Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NUZ
- Type
- protein
- Length
- 1,151 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- EOD01 heavy chain; EOD01 light chain; Pre-glycoprotein polyprotein gp complex
- UniProt
- C1K9J9
- Ligands
- MAN, NAG, BMA
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H | EOD01 heavy chain | protein | 215 | 10% helix, 54% strand | — |
| B | EOD01 light chain | protein | 218 | 6% helix, 52% strand | — |
| C, D | Pre-glycoprotein polyprotein gp complex | protein | 142 | 26% helix, 25% strand | C1K9J9 |
| L | EOD01 light chain | protein | 219 | 5% helix, 52% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains C, H, D, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, A, D, H
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains H
- GOL · Glycerol · additive · 11 copies · chains A, B, H, C, L, D
- IPA · Isopropyl alcohol · additive · 6 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.64 | 0.76 | 54 | NAG, GOL |
| 2 | 451 | 0.62 | 0.76 | 52 | GOL |
| 3 | 384 | 0.57 | 0.75 | 53 | empty |
| 4 | 335 | 0.55 | 0.75 | 54 | IPA |
| 5 | 86 | 0.38 | 0.77 | 15 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1798 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 1779 Ų buried · 22 hydrogen bonds · protein-protein
- H–D · 386 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 371 Ų buried · 7 hydrogen bonds · protein-protein
- B–L · 291 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5NUZ · Junin virus GP1 glycoprotein in complex with an antibody Fab 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 C1K9J9
- Elsewhere: RCSB PDB 5NUZ · PDBe 5NUZ · UniProt C1K9J9
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