Research workbench
Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins
Analyse Structure-based design of prefusion-stabilized human metapneumovirus fusion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SEJ
- Type
- protein
- Length
- 865 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F2 subunit; Fusion glycoprotein F1 subunit
- UniProt
- H6X1Z0
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Fusion glycoprotein F2 subunit | protein | 80 | 39% helix, 35% strand | H6X1Z0 |
| F | Fusion glycoprotein F1 subunit | protein | 356 | 31% helix, 36% strand | H6X1Z0 |
| C | Fusion glycoprotein F2 subunit | protein | 73 | 33% helix, 38% strand | H6X1Z0 |
| A | Fusion glycoprotein F1 subunit | protein | 356 | 32% helix, 34% strand | H6X1Z0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains F, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.71 | 0.75 | 79 | empty |
| 2 | 536 | 0.66 | 0.77 | 51 | empty |
| 3 | 155 | 0.51 | 0.79 | 21 | empty |
| 4 | 181 | 0.48 | 0.76 | 31 | empty |
| 5 | 59 | 0.42 | 0.82 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–F · 4507 Ų buried · 100 hydrogen bonds · protein-protein
- C–A · 4270 Ų buried · 95 hydrogen bonds · protein-protein
- F–A · 568 Ų buried · 6 hydrogen bonds · protein-protein
- F–C · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7SEJ · Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins · 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 H6X1Z0
- Elsewhere: RCSB PDB 7SEJ · PDBe 7SEJ · UniProt H6X1Z0
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