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Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E

Analyse Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JTX
Type: protein
Length: 2,908 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin
UniProt: C3W5S1
Ligands: NAG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 7 distinct chains · 24% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin	protein	323	8% helix, 39% strand	C3W5S1
B, H	Hemagglutinin	protein	162	48% helix, 15% strand	C3W5S1
C, G, I, K	Hemagglutinin	protein	322	8% helix, 39% strand	C3W5S1
D	Hemagglutinin	protein	164	47% helix, 16% strand	C3W5S1
E	Hemagglutinin	protein	321	8% helix, 40% strand	C3W5S1
F, L	Hemagglutinin	protein	161	48% helix, 16% strand	C3W5S1
J	Hemagglutinin	protein	166	46% helix, 16% strand	C3W5S1

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, C, I, E, G, K

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	192	0.83	0.97	23	empty
2	193	0.83	0.96	23	empty
3	1166	0.80	0.82	118	empty
4	535	0.79	0.85	68	empty
5	102	0.77	0.97	32	empty

Interfaces

34 interfaces between chains.

A–B · 2840 Å² buried · 42 hydrogen bonds · protein-protein
K–L · 2839 Å² buried · 36 hydrogen bonds · protein-protein
E–F · 2811 Å² buried · 40 hydrogen bonds · protein-protein
I–J · 2806 Å² buried · 39 hydrogen bonds · protein-protein
G–H · 2805 Å² buried · 42 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

4JTX · Crystal structure of 2009 pandemic influenza virus hemagglutinin mutant D225E · 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 C3W5S1
Elsewhere: RCSB PDB 4JTX · PDBe 4JTX · UniProt C3W5S1

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