Research workbench
Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin
Analyse Crystal structure of Fab 3.1 in complex with the 1918 influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PY8
- Type
- protein
- Length
- 930 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Antibody 3.1 heavy chain; Antibody 3.1…
- UniProt
- Q9WFX3
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 328 | 9% helix, 39% strand | Q9WFX3 |
| B | Hemagglutinin HA2 chain | protein | 171 | 56% helix, 12% strand | Q9WFX3 |
| I | Antibody 3.1 heavy chain | protein | 219 | 6% helix, 47% strand | — |
| J | Antibody 3.1 light chain | protein | 212 | 7% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- MLI · Malonate ion · additive · 2 copies · chains B, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.64 | 0.76 | 59 | empty |
| 2 | 437 | 0.58 | 0.74 | 57 | empty |
| 3 | 367 | 0.56 | 0.75 | 49 | MLI |
| 4 | 92 | 0.55 | 0.85 | 21 | empty |
| 5 | 116 | 0.40 | 0.75 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2636 Ų buried · 40 hydrogen bonds · protein-protein
- I–J · 1705 Ų buried · 9 hydrogen bonds · protein-protein
- B–I · 552 Ų buried · 6 hydrogen bonds · protein-protein
- A–I · 416 Ų buried · 4 hydrogen bonds · protein-protein
- B–J · 69 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 4PY8 · Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin · 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 Q9WFX3
- Elsewhere: RCSB PDB 4PY8 · PDBe 4PY8 · UniProt Q9WFX3
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