MolNFT v1 · #150016 · protein
Crystal structure of GP1 domain of lujo virus in complex with the first cub domain of neuropilin-2
6GH8 · Glycoprotein: “Crystal structure of GP1 domain of lujo virus in complex with the first cub domain of neuropilin-2”. X-ray diffraction, 2 ligands (NAG, CA), 3 pockets (best druggability 0.38). MolNFT v1 #150016 on GenesisL1: 3D…
- PDB
- 6GH8
- Type
- protein
- Length
- 460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein; Neuropilin-2
- UniProt
- C5ILC1, O60462
- Ligands
- NAG, CA
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Glycoprotein | protein | 110 | 30% helix, 27% strand | C5ILC1 |
| A, C | Neuropilin-2 | protein | 120 | 0% helix, 43% strand | O60462 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains D, A, B, C
- CA · Calcium ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.38 | 0.77 | 19 | empty |
| 2 | 52 | 0.30 | 0.76 | 12 | empty |
| 3 | 50 | 0.30 | 0.76 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 643 Ų buried · 14 hydrogen bonds · protein-protein
- D–A · 616 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6GH8 · Crystal structure of GP1 domain of Lujo virus in complex with the first CUB domain of… · the same entry in another collection · chain D against D, TM-score 1.00
- O60462 · AlphaFold monomer V2.0 prediction for neuropilin-2 (O60462) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 C5ILC1
- Every structure of UniProt O60462
- Elsewhere: RCSB PDB 6GH8 · PDBe 6GH8 · UniProt C5ILC1 · UniProt O60462
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