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Crystal structure of GP1 receptor binding domain from morogoro virus
Analyse Crystal structure of GP1 receptor binding domain from morogoro virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NFF
- Type
- protein
- Length
- 2,496 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoprotein
- UniProt
- C6ZK00
- Ligands
- NAG, MAN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D, E, F, G, H, I, J, K, L, M, N, O, P | Glycoprotein | protein | 156 | 22% helix, 31% strand | C6ZK00 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains B, F, H, O, A, C, D, E, G, I, J, K, L
- MAN · alpha-D-mannopyranose · sugar · 5 copies · chains G, H, O
- CIT · Citric acid · additive · 6 copies · chains B, C, F, E, I, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.79 | 0.85 | 45 | empty |
| 2 | 535 | 0.79 | 0.85 | 45 | CIT |
| 3 | 587 | 0.78 | 0.84 | 48 | CIT |
| 4 | 613 | 0.78 | 0.83 | 50 | empty |
| 5 | 577 | 0.77 | 0.84 | 52 | empty |
Interfaces
18 interfaces between chains.
- E–F · 923 Ų buried · 7 hydrogen bonds · protein-protein
- I–L · 922 Ų buried · 8 hydrogen bonds · protein-protein
- D–H · 884 Ų buried · 10 hydrogen bonds · protein-protein
- J–K · 867 Ų buried · 12 hydrogen bonds · protein-protein
- N–P · 867 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 5NFF · Crystal structure of GP1 receptor binding domain from Morogoro virus · the same entry in another collection · chain B against B, 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 C6ZK00
- Elsewhere: RCSB PDB 5NFF · PDBe 5NFF · UniProt C6ZK00
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