MolNFT v1 · #166904 · protein
Structure of human 1G05 Fab in complex with influenza virus neuraminidase from B/PHUKET/3073/2013
6V4N: “Structure of human 1G05 Fab in complex with influenza virus neuraminidase from B/PHUKET/3073/2013”. Electron microscopy, 3 ligands (NAG, BMA, CA), 20 pockets (best druggability 0.79). MolNFT v1 #166904 on GenesisL1: 3D structure…
- PDB
- 6V4N
- Type
- protein
- Length
- 3,286 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase; Antibody Fab heavy chain; Antibody Fab light chain
- EC
- 3.2.1.18
- UniProt
- A0A4P8YQ63
- Ligands
- NAG, BMA, CA
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, N | Neuraminidase (EC 3.2.1.18) | protein | 390 | 2% helix, 49% strand | A0A4P8YQ63 |
| M, W | Neuraminidase (EC 3.2.1.18) | protein | 391 | 1% helix, 49% strand | A0A4P8YQ63 |
| A, C, D, H | Antibody Fab heavy chain | protein | 218 | 3% helix, 52% strand | — |
| B, E, G, L | Antibody Fab light chain | protein | 213 | 6% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains I, B, M, G, N, L, W, E
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains B, I, L, W, N
- CA · Calcium ion · metal · 4 copies · chains I, M, N, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.79 | 0.96 | 31 | empty |
| 2 | 102 | 0.77 | 0.97 | 24 | empty |
| 3 | 812 | 0.75 | 0.79 | 139 | empty |
| 4 | 164 | 0.75 | 0.92 | 32 | empty |
| 5 | 179 | 0.75 | 0.92 | 33 | empty |
Interfaces
18 interfaces between chains.
- I–M · 1973 Ų buried · 21 hydrogen bonds · protein-protein
- M–N · 1962 Ų buried · 21 hydrogen bonds · protein-protein
- N–W · 1958 Ų buried · 18 hydrogen bonds · protein-protein
- I–W · 1948 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1809 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6V4N · Structure of human 1G05 Fab in complex with influenza virus neuraminidase from… · the same entry in another collection · chain I against I, 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 A0A4P8YQ63
- Elsewhere: RCSB PDB 6V4N · PDBe 6V4N · UniProt A0A4P8YQ63
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