MolNFT v1 · #158424 · protein

Crystal structure of a computationally optimized H5 influenza hemagglutinin

6NTF: “Crystal structure of a computationally optimized H5 influenza hemagglutinin”. X-ray diffraction, 2 ligands (NAG, MG), 5 pockets (best druggability 0.59). MolNFT v1 #158424 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6NTF
Type: protein
Length: 491 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin
Ligands: NAG, MG
Pockets: 5 · best druggability 0.59

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin	protein	491	22% helix, 30% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
MG · Magnesium ion · metal · 4 copies · chains A
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	342	0.59	0.77	42	empty
2	66	0.38	0.79	16	empty
3	57	0.36	0.79	16	empty
4	50	0.34	0.78	16	PEG
5	61	0.31	0.75	15	empty

Modifications

Observed in the structure: 5 disulfide, 5 glycan, 1 covalent (disulfide, N-glycosylation, additive adduct).

Compared structures

6NTF · Crystal structure of a computationally optimized H5 influenza hemagglutinin · 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 6NTF · PDBe 6NTF

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