MolNFT v1 · #16218 · protein

Influenza B virus neuraminidase can synthesize its own inhibitor

1NSD: “Influenza B virus neuraminidase can synthesize its own inhibitor”. X-ray diffraction, 3 ligands (DAN, NAG, CA), 5 pockets (best druggability 0.79). MolNFT v1 #16218 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1NSD
Type: protein
Length: 780 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuraminidase
EC: 3.2.1.18
UniProt: P27907
Ligands: DAN, NAG, CA
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 2% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Neuraminidase (EC 3.2.1.18)	protein	390	2% helix, 48% strand	P27907

Ligands and binding sites

DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
CA · Calcium ion · metal · 3 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	126	0.79	0.98	29	empty
2	126	0.79	0.97	29	empty
3	189	0.58	0.81	27	DAN
4	170	0.56	0.81	29	DAN
5	200	0.51	0.77	43	empty

Interfaces

1 interface between chains.

A–B · 1997 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

1NSD · Influenza B virus neuraminidase can synthesize its own inhibitor · the same entry in another collection · chain B against B, 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 P27907
Elsewhere: RCSB PDB 1NSD · PDBe 1NSD · UniProt P27907

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