MolNFT v1 · #51820 · protein
Influenza virus hemagglutinin complexed with a neutralizing antibody
2VIR · Immunoglobulin (IGG1, lambda): “Influenza virus hemagglutinin complexed with a neutralizing antibody”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.66). MolNFT v1 #51820 on GenesisL1: 3D structure, binding sites…
- PDB
- 2VIR
- Type
- protein
- Length
- 698 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin (IGG1, lambda); Hemagglutinin
- UniProt
- P03437
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin (IGG1, lambda) | protein | 210 | 8% helix, 52% strand | — |
| B | Immunoglobulin (IGG1, lambda) | protein | 221 | 5% helix, 52% strand | — |
| C | Hemagglutinin | protein | 267 | 12% helix, 39% strand | P03437 |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.66 | 0.79 | 55 | empty |
| 2 | 494 | 0.59 | 0.74 | 59 | empty |
| 3 | 231 | 0.53 | 0.77 | 26 | empty |
| 4 | 56 | 0.41 | 0.82 | 18 | empty |
| 5 | 64 | 0.31 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1847 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 662 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 54 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2VIR · Influenza virus hemagglutinin complexed with a neutralizing 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 P03437
- Elsewhere: RCSB PDB 2VIR · PDBe 2VIR · UniProt P03437
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