MolNFT v1 · #161044 · protein
Crystal structure of human 1G04 Fab in complex with influenza virus neuraminidase from A/HUNAN/02650/2016 (H7N9)
6Q1Z: “Crystal structure of human 1G04 Fab in complex with influenza virus neuraminidase from A/HUNAN/02650/2016…”. X-ray diffraction, 4 ligands (MAN, NAG, BMA), 13 pockets (best druggability 0.69). MolNFT v1 #161044 on GenesisL1: 3D…
- PDB
- 6Q1Z
- Type
- protein
- Length
- 1,660 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; 1G04 Fab kappa light chain; 1G04 Fab IGG1 heavy chain
- EC
- 3.2.1.18
- Ligands
- MAN, NAG, BMA, CA
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase (EC 3.2.1.18) | protein | 388 | 4% helix, 45% strand | — |
| L, C | 1G04 Fab kappa light chain | protein | 215 | 6% helix, 51% strand | — |
| H, D | 1G04 Fab IGG1 heavy chain | protein | 227 | 5% helix, 52% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 16 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, L, B, C
- BMA · beta-D-mannopyranose · sugar · 4 copies
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.69 | 0.95 | 23 | empty |
| 2 | 60 | 0.68 | 0.96 | 24 | empty |
| 3 | 189 | 0.68 | 0.87 | 44 | empty |
| 4 | 188 | 0.64 | 0.84 | 42 | empty |
| 5 | 301 | 0.62 | 0.79 | 35 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2132 Ų buried · 17 hydrogen bonds · protein-protein
- L–H · 2041 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 1112 Ų buried · 19 hydrogen bonds · protein-protein
- A–H · 1103 Ų buried · 18 hydrogen bonds · protein-protein
- A–L · 187 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 26 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q1Z · Crystal structure of human 1G04 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
- Elsewhere: RCSB PDB 6Q1Z · PDBe 6Q1Z
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