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Crystal structure of Z2B3 D102R Fab in complex with influenza virus neuraminidase from A/Serbia/NS-601/2014 (H1N1)
Analyse Crystal structure of Z2B3 D102R 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
- 6LXK
- Type
- protein
- Length
- 2,877 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.608
- Source
- Homo sapiens; Influenza A virus
- Molecule
- Neuraminidase; Heavy chain of Z2B3-D102R Fab; Light chain of Z2B3-D102R Fab
- EC
- 3.2.1.18
- UniProt
- X2L845
- Ligands
- NAG, BMA, CA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · resolution 3.608 · 3 distinct chains · 5% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 387 | 4% helix, 44% strand | X2L845 |
| H, E, J | Heavy chain of Z2B3-D102R Fab | protein | 232 | 5% helix, 48% strand | — |
| L, F, K | Light chain of Z2B3-D102R Fab | protein | 211 | 7% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, H, B, D, J, E
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains H, J, E
- CA · Calcium ion · metal · 8 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.73 | 0.81 | 68 | empty |
| 2 | 500 | 0.72 | 0.81 | 60 | empty |
| 3 | 365 | 0.70 | 0.82 | 46 | empty |
| 4 | 214 | 0.59 | 0.81 | 36 | empty |
| 5 | 362 | 0.59 | 0.76 | 49 | empty |
Interfaces
15 interfaces between chains.
- J–K · 1754 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1685 Ų buried · 18 hydrogen bonds · protein-protein
- H–L · 1646 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1621 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1602 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6LXK · Crystal structure of Z2B3 D102R 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 X2L845
- Elsewhere: RCSB PDB 6LXK · PDBe 6LXK · UniProt X2L845
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