MolNFT v1 · #104022 · protein
Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin
4PY8 · Hemagglutinin HA1 chain: “Crystal structure of Fab 3.1 in complex with the 1918 influenza virus hemagglutinin”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.64). MolNFT v1 #104022 on GenesisL1: 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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