Research workbench
Cryoem derived model of na-80 Fab in complex with N9 SHANGHAI2
Analyse Cryoem derived model of na-80 Fab in complex with N9 SHANGHAI2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PZZ
- Type
- protein
- Length
- 2,464 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; Na-80 fragment antibody light chain; Na-80 fragment antibody heavy chain
- EC
- 3.2.1.18
- UniProt
- S5MF06
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 3 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase (EC 3.2.1.18) | protein | 388 | 4% helix, 43% strand | S5MF06 |
| L, E, G, J | Na-80 fragment antibody light chain | protein | 108 | 0% helix, 48% strand | — |
| H, F, I, K | Na-80 fragment antibody heavy chain | protein | 120 | 8% helix, 48% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 24 copies · chains D, A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, D, B, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.72 | 0.98 | 22 | empty |
| 2 | 65 | 0.71 | 0.97 | 25 | empty |
| 3 | 58 | 0.69 | 0.97 | 20 | empty |
| 4 | 64 | 0.69 | 0.96 | 22 | empty |
| 5 | 307 | 0.56 | 0.77 | 43 | empty |
Interfaces
16 interfaces between chains.
- A–D · 1593 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1592 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1592 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1590 Ų buried · 14 hydrogen bonds · protein-protein
- G–I · 745 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6PZZ · CryoEM derived model of NA-80 Fab in complex with N9 Shanghai2 · 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 S5MF06
- Elsewhere: RCSB PDB 6PZZ · PDBe 6PZZ · UniProt S5MF06
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