Research workbench
Crystal structure of human 1G01 Fab in complex with influenza virus neuraminidase from A/CALIFORNIA/04/2009 (H1N1)
Analyse Crystal structure of human 1G01 Fab in complex with influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q23
- Type
- protein
- Length
- 3,304 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; 1G01 Fab IGG1 heavy chain; 1G01 Fab kappa light chain
- EC
- 3.2.1.18
- UniProt
- C5MQL2
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, A, D | Neuraminidase (EC 3.2.1.18) | protein | 384 | 3% helix, 47% strand | C5MQL2 |
| H, E, G, J | 1G01 Fab IGG1 heavy chain | protein | 227 | 7% helix, 51% strand | — |
| L, F, I, K | 1G01 Fab kappa light chain | protein | 215 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, B, A, D
- CA · Calcium ion · metal · 9 copies · chains C, B, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.70 | 0.81 | 69 | empty |
| 2 | 794 | 0.68 | 0.76 | 70 | empty |
| 3 | 775 | 0.67 | 0.75 | 75 | empty |
| 4 | 662 | 0.67 | 0.76 | 58 | empty |
| 5 | 677 | 0.66 | 0.75 | 63 | empty |
Interfaces
22 interfaces between chains.
- J–K · 2106 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 2105 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 2067 Ų buried · 12 hydrogen bonds · protein-protein
- G–I · 2056 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1606 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q23 · Crystal structure of human 1G01 Fab in complex with influenza virus neuraminidase from… · the same entry in another collection · chain C against C, 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 C5MQL2
- Elsewhere: RCSB PDB 6Q23 · PDBe 6Q23 · UniProt C5MQL2
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