MolNFT v1 · #169971 · protein
Cryo-EM structure of vaccine-elicited rhesus antibody 789-203-3C12 in complex with stabilized SI06 (A/SOLOMON ISLANDS/3/06) influenza hemagglutinin trimer
6XSK · 789-203-3C12 Fab light chain: “Cryo-EM structure of vaccine-elicited rhesus antibody 789-203-3C12 in complex with stabilized SI06 (A/SOLOMON…”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.83). MolNFT…
- PDB
- 6XSK
- Type
- protein
- Length
- 2,163 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 789-203-3C12 Fab light chain; 789-203-3C12 Fab heavy chain; Hemagglutinin HA1 chain…
- UniProt
- A7Y8I1
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, J, K | 789-203-3C12 Fab light chain | protein | 107 | 3% helix, 49% strand | — |
| H, G, I | 789-203-3C12 Fab heavy chain | protein | 125 | 5% helix, 47% strand | — |
| A, C, E | Hemagglutinin HA1 chain | protein | 322 | 9% helix, 35% strand | A7Y8I1 |
| B, D, F | Hemagglutinin HA2 chain | protein | 167 | 54% helix, 11% strand | A7Y8I1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, C, E, I, B, D, G, H, F
- 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.83 | 0.94 | 39 | empty |
| 2 | 1069 | 0.76 | 0.78 | 99 | empty |
| 3 | 433 | 0.69 | 0.80 | 69 | empty |
| 4 | 259 | 0.68 | 0.84 | 43 | empty |
| 5 | 214 | 0.68 | 0.85 | 35 | empty |
Interfaces
27 interfaces between chains.
- C–D · 2787 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2786 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2783 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 1118 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1113 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 disulfide, 24 glycan (disulfide, N-glycosylation).
Compared structures
- 6XSK · Cryo-EM Structure of Vaccine-Elicited Rhesus Antibody 789-203-3C12 in Complex with… · the same entry in another collection · chain L against L, 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 A7Y8I1
- Elsewhere: RCSB PDB 6XSK · PDBe 6XSK · UniProt A7Y8I1
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