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Crystal structure of vaccine-elicited receptor-binding site targeting antibody lpaf-A.01 in complex with hemagglutinin H1 A/CALIFORNIA/04/2009
Analyse Crystal structure of vaccine-elicited receptor-binding site targeting antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6URM
- Type
- protein
- Length
- 1,303 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; The heavy chain of antibody lpaf-A.01; The light chain of antibody…
- UniProt
- A0A3S7XTA4
- Ligands
- NAG, MAN, SO4
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Hemagglutinin | protein | 219 | 10% helix, 37% strand | A0A3S7XTA4 |
| H, D | The heavy chain of antibody lpaf-A.01 | protein | 224 | 4% helix, 50% strand | — |
| L | The light chain of antibody lpaf-A.01 | protein | 210 | 8% helix, 50% strand | — |
| C | Hemagglutinin | protein | 217 | 10% helix, 35% strand | A0A3S7XTA4 |
| E | The light chain of antibody lpaf-A.01 | protein | 209 | 8% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains H, L, D, E, F
- MAN · alpha-D-mannopyranose · sugar · chains D
- SO4 · Sulfate ion · ion · 4 copies · chains F, H, L, D, E
- GOL · Glycerol · additive · 2 copies · chains F, H, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.78 | 0.80 | 118 | GOL |
| 2 | 74 | 0.70 | 0.95 | 23 | empty |
| 3 | 245 | 0.68 | 0.84 | 43 | empty |
| 4 | 391 | 0.67 | 0.80 | 45 | empty |
| 5 | 270 | 0.63 | 0.80 | 34 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1931 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 1906 Ų buried · 23 hydrogen bonds · protein-protein
- F–C · 633 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 456 Ų buried · 12 hydrogen bonds · protein-protein
- F–H · 455 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6URM · Crystal structure of vaccine-elicited receptor-binding site targeting antibody LPAF-a.01… · the same entry in another collection · chain F against F, 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 A0A3S7XTA4
- Elsewhere: RCSB PDB 6URM · PDBe 6URM · UniProt A0A3S7XTA4
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