MolNFT v1 · #76615 · protein

Crystal structure of HA2 R106H mutant of H2 hemagglutinin, neutral pH form

3QQB: “Crystal structure of HA2 R106H mutant of H2 hemagglutinin, neutral pH form”. X-ray diffraction, 1 ligand (NAG), 5 pockets (best druggability 0.63). MolNFT v1 #76615 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3QQB
Type: protein
Length: 496 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin
UniProt: C7S226
Ligands: NAG
Pockets: 5 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 26% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin	protein	324	10% helix, 40% strand	C7S226
B	Hemagglutinin	protein	172	57% helix, 13% strand	C7S226

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A
PEG · Di(hydroxyethyl)ether · additive · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	339	0.63	0.79	44	empty
2	56	0.37	0.80	12	empty
3	67	0.33	0.76	16	empty
4	81	0.32	0.74	19	empty
5	50	0.27	0.74	18	empty

Interfaces

1 interface between chains.

A–B · 2588 Å² buried · 40 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

3QQB · Crystal structure of HA2 R106H mutant of H2 hemagglutinin, neutral pH form · 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 C7S226
Elsewhere: RCSB PDB 3QQB · PDBe 3QQB · UniProt C7S226

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