Research workbench
Cryo-EM structure of the VRC310 clinical trial, vaccine-elicited, human antibody 310-030-1D06 Fab in complex with an H1 NC99 ha trimer
Analyse Cryo-EM structure of the VRC310 clinical trial, vaccine-elicited, human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MFG
- Type
- protein
- Length
- 2,121 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; 310-030-1D06 heavy; 310-030-1D06 light
- UniProt
- Q6WG00, Q289M7
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 4 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Hemagglutinin HA1 chain | protein | 322 | 11% helix, 34% strand | Q6WG00 |
| B, D, I | Hemagglutinin HA2 chain | protein | 157 | 55% helix, 10% strand | Q289M7 |
| H, E, J | 310-030-1D06 heavy | protein | 120 | 5% helix, 37% strand | — |
| L, F, K | 310-030-1D06 light | protein | 108 | 0% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains B, D, I, A, C, G
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains L, F, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.72 | 0.80 | 56 | empty |
| 2 | 390 | 0.71 | 0.82 | 52 | empty |
| 3 | 517 | 0.70 | 0.80 | 57 | empty |
| 4 | 303 | 0.66 | 0.82 | 47 | empty |
| 5 | 296 | 0.66 | 0.82 | 47 | empty |
Interfaces
27 interfaces between chains.
- C–D · 2590 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 2581 Ų buried · 38 hydrogen bonds · protein-protein
- G–I · 2580 Ų buried · 34 hydrogen bonds · protein-protein
- D–I · 945 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 942 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 7MFG · Cryo-EM structure of the VRC310 clinical trial, vaccine-elicited, human antibody… · 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 Q6WG00
- Every structure of UniProt Q289M7
- Elsewhere: RCSB PDB 7MFG · PDBe 7MFG · UniProt Q6WG00 · UniProt Q289M7
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