MolNFT v1 · #160959 · protein
Crystal structure of human na-63 Fab in complex with neuraminidase from A/HUNAN/02650/2016(H7N9)
6PZF: “Crystal structure of human na-63 Fab in complex with neuraminidase from A/HUNAN/02650/2016(H7N9)”. X-ray diffraction, 5 ligands (MAN, NAG, BMA), 12 pockets (best druggability 0.66). MolNFT v1 #160959 on GenesisL1: 3D structure…
- PDB
- 6PZF
- Type
- protein
- Length
- 1,632 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; Na-63 Fab light chain; Na-63 Fab heavy chain
- EC
- 3.2.1.18
- Ligands
- MAN, NAG, BMA, CA, PO4
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Neuraminidase (EC 3.2.1.18) | protein | 388 | 4% helix, 45% strand | — |
| E, L | Na-63 Fab light chain | protein | 215 | 5% helix, 52% strand | — |
| F, H | Na-63 Fab heavy chain | protein | 213 | 10% helix, 54% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 16 copies
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains B, A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- CA · Calcium ion · metal · 2 copies · chains B, A
- PO4 · Phosphate ion · ion · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.66 | 0.74 | 85 | empty |
| 2 | 667 | 0.64 | 0.74 | 52 | empty |
| 3 | 282 | 0.62 | 0.80 | 38 | PO4 |
| 4 | 278 | 0.61 | 0.80 | 45 | PO4 |
| 5 | 243 | 0.53 | 0.76 | 34 | empty |
Interfaces
7 interfaces between chains.
- L–H · 1851 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1848 Ų buried · 16 hydrogen bonds · protein-protein
- F–H · 518 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 381 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 353 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6PZF · Crystal structure of human NA-63 Fab in complex with neuraminidase from… · the same entry in another collection · chain B against B, 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 6PZF · PDBe 6PZF
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