MolNFT v1 · #187443 · protein
Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins
7SEM · MPE8 Fab heavy chain: “Structure-based design of prefusion-stabilized human metapneumovirus fusion proteins”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.77). MolNFT v1 #187443 on GenesisL1: 3D structure…
- PDB
- 7SEM
- Type
- protein
- Length
- 848 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MPE8 Fab heavy chain; Fusion glycoprotein F0; MPE8 Fab light chain
- UniProt
- H6X1Z0
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | MPE8 Fab heavy chain | protein | 214 | 6% helix, 49% strand | — |
| F | Fusion glycoprotein F0 | protein | 430 | 32% helix, 36% strand | H6X1Z0 |
| C | MPE8 Fab light chain | protein | 204 | 10% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.77 | 0.88 | 44 | empty |
| 2 | 137 | 0.49 | 0.79 | 22 | empty |
| 3 | 132 | 0.48 | 0.78 | 22 | empty |
| 4 | 217 | 0.46 | 0.74 | 39 | empty |
| 5 | 53 | 0.43 | 0.84 | 20 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1789 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 777 Ų buried · 15 hydrogen bonds · protein-protein
- F–C · 230 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7SEM · 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 7SEM · PDBe 7SEM · UniProt H6X1Z0
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