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Crystal structure of human Z2B3 Fab in complex with influenza virus neuraminidase from A/Anhui/1/2013 (H7N9)
Analyse Crystal structure of human Z2B3 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
- 6LXJ
- Type
- protein
- Length
- 3,238 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.903
- Source
- Homo sapiens; Influenza A virus (A/Anhui/1-BALF_RG44/2013(H7N9))
- Molecule
- Neuraminidase; Heavy chain of Z2B3 Fab; Light chain of Z2B3 Fab
- EC
- 3.2.1.18
- UniProt
- A0A024E1X5
- Ligands
- MAN, NAG, BMA, CA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.903 · 9 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 388 | 5% helix, 44% strand | A0A024E1X5 |
| H | Heavy chain of Z2B3 Fab | protein | 226 | 5% helix, 51% strand | — |
| L | Light chain of Z2B3 Fab | protein | 213 | 9% helix, 49% strand | — |
| E | Heavy chain of Z2B3 Fab | protein | 214 | 6% helix, 49% strand | — |
| F | Light chain of Z2B3 Fab | protein | 207 | 5% helix, 51% strand | — |
| J | Heavy chain of Z2B3 Fab | protein | 206 | 6% helix, 51% strand | — |
| K | Light chain of Z2B3 Fab | protein | 204 | 6% helix, 53% strand | — |
| M | Heavy chain of Z2B3 Fab | protein | 208 | 4% helix, 53% strand | — |
| N | Light chain of Z2B3 Fab | protein | 208 | 4% helix, 50% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 29 copies · chains H, B, E, C, J, D, M, A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, H, B, E, C, J, D, M
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains H, B, E, C, J, D, M, A
- CA · Calcium ion · metal · 4 copies · chains A, B, C, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.75 | 0.80 | 111 | empty |
| 2 | 494 | 0.74 | 0.83 | 68 | empty |
| 3 | 570 | 0.74 | 0.82 | 60 | empty |
| 4 | 512 | 0.73 | 0.82 | 62 | empty |
| 5 | 378 | 0.72 | 0.84 | 52 | empty |
Interfaces
18 interfaces between chains.
- H–L · 1721 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1708 Ų buried · 11 hydrogen bonds · protein-protein
- M–N · 1674 Ų buried · 14 hydrogen bonds · protein-protein
- J–K · 1663 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1655 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6LXJ · Crystal structure of human Z2B3 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 A0A024E1X5
- Elsewhere: RCSB PDB 6LXJ · PDBe 6LXJ · UniProt A0A024E1X5
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