MolNFT v1 · #104868 · protein
Crystal structure of the 2009 pandemic H1N1 influenza virus neuraminidase with a neutralizing antibody
4QNP: “Crystal structure of the 2009 pandemic H1N1 influenza virus neuraminidase with a neutralizing antibody”. X-ray diffraction, 2 ligands (NAG, CA), 18 pockets (best druggability 0.64). MolNFT v1 #104868 on GenesisL1: 3D structure…
- PDB
- 4QNP
- Type
- protein
- Length
- 1,643 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; Neutralizing antibody, light chain; Neutralizing antibody, heavy chain
- EC
- 3.2.1.18
- UniProt
- S5N0T0
- Ligands
- NAG, CA
- Pockets
- 18 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase (EC 3.2.1.18) | protein | 386 | 3% helix, 45% strand | S5N0T0 |
| F | Neutralizing antibody, light chain | protein | 212 | 6% helix, 50% strand | — |
| E, H | Neutralizing antibody, heavy chain | protein | 224 | 9% helix, 50% strand | — |
| L | Neutralizing antibody, light chain | protein | 211 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.64 | 0.79 | 52 | empty |
| 2 | 455 | 0.63 | 0.76 | 45 | empty |
| 3 | 388 | 0.62 | 0.77 | 34 | empty |
| 4 | 234 | 0.60 | 0.81 | 38 | empty |
| 5 | 424 | 0.59 | 0.75 | 53 | empty |
Interfaces
8 interfaces between chains.
- F–E · 1973 Ų buried · 22 hydrogen bonds · protein-protein
- L–H · 1875 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1593 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 557 Ų buried · 5 hydrogen bonds · protein-protein
- B–L · 457 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4QNP · Crystal structure of the 2009 pandemic H1N1 influenza virus neuraminidase with a… · 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 S5N0T0
- Elsewhere: RCSB PDB 4QNP · PDBe 4QNP · UniProt S5N0T0
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