Research workbench
Cryo-EM structure of the neutralizing antibody MPV467 in complex with prefusion human metapneumovirus F glycoprotein
Analyse Cryo-EM structure of the neutralizing antibody MPV467 in complex with prefusion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UR4
- Type
- protein
- Length
- 1,974 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusion glycoprotein F0; MPV467 Fab heavy chain; MPV467 Fab light chain
- UniProt
- H6X1Z1
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 21% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Fusion glycoprotein F0 | protein | 431 | 29% helix, 35% strand | H6X1Z1 |
| F, H, I | MPV467 Fab heavy chain | protein | 121 | 5% helix, 43% strand | — |
| G, J, L | MPV467 Fab light chain | protein | 106 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.84 | 0.86 | 113 | empty |
| 2 | 774 | 0.84 | 0.87 | 78 | empty |
| 3 | 442 | 0.80 | 0.88 | 64 | empty |
| 4 | 340 | 0.79 | 0.89 | 57 | empty |
| 5 | 80 | 0.73 | 0.96 | 20 | empty |
Interfaces
12 interfaces between chains.
- A–B · 2281 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 2279 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 2234 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 983 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 973 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 7UR4 · Cryo-EM Structure of the Neutralizing Antibody MPV467 in Complex with Prefusion Human… · 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 H6X1Z1
- Elsewhere: RCSB PDB 7UR4 · PDBe 7UR4 · UniProt H6X1Z1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.