MolNFT v1 · #112374 · protein
Crystal structure of GP1 - the receptor binding domain of lassa virus
4ZJF · Glycoprotein: “Crystal structure of GP1 - the receptor binding domain of lassa virus”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.61). MolNFT v1 #112374 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4ZJF
- Type
- protein
- Length
- 636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein
- UniProt
- A0A097F5U5
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glycoprotein | protein | 161 | 22% helix, 29% strand | A0A097F5U5 |
| B, D | Glycoprotein | protein | 157 | 22% helix, 28% strand | A0A097F5U5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B, D, 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 | 290 | 0.61 | 0.80 | 39 | empty |
| 2 | 273 | 0.61 | 0.80 | 36 | empty |
| 3 | 103 | 0.38 | 0.75 | 24 | empty |
| 4 | 92 | 0.35 | 0.74 | 20 | empty |
| 5 | 103 | 0.33 | 0.73 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 509 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 496 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 308 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 289 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 4ZJF · Crystal structure of GP1 - the receptor binding domain of Lassa virus · 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 A0A097F5U5
- Elsewhere: RCSB PDB 4ZJF · PDBe 4ZJF · UniProt A0A097F5U5
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