MolNFT v1 · #161045 · protein
Crystal structure of human 1E01 Fab in complex with influenza virus neuraminidase from A/JAPAN/305/1957 (H2N2)
6Q20: “Crystal structure of human 1E01 Fab in complex with influenza virus neuraminidase from A/JAPAN/305/1957 (H2N2)”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 8 pockets (best druggability 0.70). MolNFT v1 #161045 on GenesisL1: 3D…
- PDB
- 6Q20
- Type
- protein
- Length
- 830 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; 1E01 Fab kappa light chain; 1E01 Fab IGG1 heavy chain
- EC
- 3.2.1.18
- UniProt
- C7RWN0
- Ligands
- NAG, MAN, BMA, CA
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuraminidase (EC 3.2.1.18) | protein | 388 | 3% helix, 47% strand | C7RWN0 |
| L | 1E01 Fab kappa light chain | protein | 215 | 6% helix, 50% strand | — |
| H | 1E01 Fab IGG1 heavy chain | protein | 227 | 5% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, L
- MAN · alpha-D-mannopyranose · sugar · 4 copies
- BMA · beta-D-mannopyranose · sugar
- CA · Calcium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.70 | 0.85 | 49 | empty |
| 2 | 321 | 0.61 | 0.78 | 35 | empty |
| 3 | 57 | 0.54 | 0.89 | 23 | empty |
| 4 | 196 | 0.49 | 0.76 | 31 | empty |
| 5 | 149 | 0.39 | 0.73 | 25 | empty |
Interfaces
3 interfaces between chains.
- L–H · 2095 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 956 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 202 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q20 · Crystal structure of human 1E01 Fab in complex with influenza virus neuraminidase from… · 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 C7RWN0
- Elsewhere: RCSB PDB 6Q20 · PDBe 6Q20 · UniProt C7RWN0
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