MolNFT v1 · #93349 · protein
N2 neuraminidase D151G mutant of A/TANZANIA/205/2010 H3N2 in complex with hepes
4GZS: “N2 neuraminidase D151G mutant of A/TANZANIA/205/2010 H3N2 in complex with hepes”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 12 pockets (best druggability 0.81). MolNFT v1 #93349 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4GZS
- Type
- protein
- Length
- 1,552 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- Ligands
- NAG, MAN, BMA, FUC, CA
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Neuraminidase | protein | 388 | 4% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, D, B, C
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains D, A, B, C
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains D, A, B, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 5 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
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1077 | 0.81 | 0.82 | 115 | empty |
| 2 | 322 | 0.59 | 0.78 | 43 | EPE |
| 3 | 286 | 0.58 | 0.78 | 32 | EPE |
| 4 | 280 | 0.57 | 0.77 | 37 | EPE |
| 5 | 287 | 0.56 | 0.77 | 35 | EPE |
Interfaces
4 interfaces between chains.
- A–B · 1713 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1706 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1704 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 1686 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 15 glycan (disulfide, N-glycosylation).
Compared structures
- 4GZS · N2 neuraminidase D151G mutant of a/Tanzania/205/2010 H3N2 in complex with hepes · 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
- Elsewhere: RCSB PDB 4GZS · PDBe 4GZS
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