Research workbench
H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase mutant explained by kinetic and structural analysis
Analyse H1N1 2009 pandemic influenza virus: resistance of the I223R neuraminidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4B7R
- Type
- protein
- Length
- 1,548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- UniProt
- C7FH46
- Ligands
- G39, NAG, CA
- Pockets
- 13 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase | protein | 387 | 4% helix, 46% strand | C7FH46 |
Ligands and binding sites
- G39 · (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy) cyclohex-1-ene-1-carboxylic acid · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.63 | 0.81 | 48 | G39, EPE |
| 2 | 276 | 0.63 | 0.81 | 42 | G39, EPE |
| 3 | 279 | 0.63 | 0.81 | 43 | G39, EPE |
| 4 | 262 | 0.62 | 0.81 | 36 | G39, EPE |
| 5 | 375 | 0.59 | 0.76 | 48 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1647 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1602 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1596 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1586 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 22 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 4B7R · H1N1 2009 Pandemic Influenza Virus: Resistance of the I223R Neuraminidase Mutant… · 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 C7FH46
- Elsewhere: RCSB PDB 4B7R · PDBe 4B7R · UniProt C7FH46
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