MolNFT v1 · #165585 · protein
Cryoem-derived model of na-63 Fab in complex with N9 SHANGHAI2
6U02 · Neuraminidase: “Cryoem-derived model of na-63 Fab in complex with N9 SHANGHAI2”. Electron microscopy, 3 ligands (MAN, NAG, BMA), 20 pockets (best druggability 0.73). MolNFT v1 #165585 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6U02
- Type
- protein
- Length
- 2,452 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; Fab-63 light chain; Fab-63 heavy chain
- EC
- 3.2.1.18
- UniProt
- S5MF06
- Ligands
- MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 5% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, J | Neuraminidase (EC 3.2.1.18) | protein | 388 | 4% helix, 45% strand | S5MF06 |
| L, C, F, I | Fab-63 light chain | protein | 109 | 3% helix, 46% strand | — |
| H, D, G, K | Fab-63 heavy chain | protein | 116 | 10% helix, 53% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 24 copies · chains J, A, B, E
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, J, B, E
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains J, A, B, E
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 | 65 | 0.73 | 0.98 | 22 | empty |
| 2 | 56 | 0.69 | 0.96 | 19 | empty |
| 3 | 62 | 0.68 | 0.96 | 19 | empty |
| 4 | 57 | 0.67 | 0.96 | 19 | empty |
| 5 | 269 | 0.63 | 0.81 | 35 | empty |
Interfaces
16 interfaces between chains.
- A–B · 1663 Ų buried · 16 hydrogen bonds · protein-protein
- A–J · 1661 Ų buried · 16 hydrogen bonds · protein-protein
- B–E · 1658 Ų buried · 16 hydrogen bonds · protein-protein
- E–J · 1656 Ų buried · 16 hydrogen bonds · protein-protein
- L–H · 878 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6U02 · CryoEM-derived model of NA-63 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 6U02 · PDBe 6U02 · UniProt S5MF06
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