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H7 HA0 in complex with fv from H7.5 IgG

Analyse H7 HA0 in complex with fv from H7.5 IgG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MLM
Type: protein
Length: 2,121 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; Heavy chain fv of H7.5 Fab; Light chain…
UniProt: B2LVD7
Ligands: NAG
Pockets: 20 · best druggability 0.73

Structure

electron microscopy · 4 distinct chains · 18% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, H	Hemagglutinin HA1 chain	protein	311	10% helix, 38% strand	B2LVD7
C, D, J	Hemagglutinin HA2 chain	protein	168	53% helix, 8% strand	B2LVD7
E, F, K	Heavy chain fv of H7.5 Fab	protein	122	5% helix, 53% strand	—
I, G, L	Light chain fv of H7.5 Fab	protein	106	3% helix, 48% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, C, B, D, H, J

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	246	0.73	0.88	27	empty
2	268	0.73	0.87	27	empty
3	263	0.73	0.87	28	empty
4	501	0.62	0.75	58	empty
5	433	0.59	0.75	59	NAG

Interfaces

27 interfaces between chains.

H–J · 3199 Å² buried · 53 hydrogen bonds · protein-protein
A–C · 3192 Å² buried · 53 hydrogen bonds · protein-protein
B–D · 3191 Å² buried · 53 hydrogen bonds · protein-protein
K–L · 932 Å² buried · 11 hydrogen bonds · protein-protein
E–I · 932 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 9 glycan (disulfide, N-glycosylation).

Compared structures

6MLM · H7 HA0 in complex with Fv from H7.5 IgG · 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 B2LVD7
Elsewhere: RCSB PDB 6MLM · PDBe 6MLM · UniProt B2LVD7

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