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Crystal structure of Z2B3 Fab in complex with influenza virus neuraminidase from A/BREVIG MISSION/1/1918 (H1N1)

Analyse Crystal structure of Z2B3 Fab in complex with influenza virus neuraminidase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LXI
Type: protein
Length: 1,627 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neuraminidase; Heavy chain of Z2B3 Fab; Light chain of Z2B3 Fab
EC: 3.2.1.18
UniProt: Q9IGQ6
Ligands: NAG, BMA, MAN, FUC, CA
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 5% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Neuraminidase (EC 3.2.1.18)	protein	387	4% helix, 45% strand	Q9IGQ6
H	Heavy chain of Z2B3 Fab	protein	232	6% helix, 50% strand	—
L	Light chain of Z2B3 Fab	protein	211	6% helix, 49% strand	—
C	Heavy chain of Z2B3 Fab	protein	214	7% helix, 48% strand	—
D	Light chain of Z2B3 Fab	protein	196	4% helix, 46% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, H, B, C
BMA · beta-D-mannopyranose · sugar · 2 copies · chains H, C
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains H, C
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, H, B, C
CA · Calcium ion · metal · 4 copies · chains A, B

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

Pockets

14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	570	0.74	0.81	66	empty
2	68	0.72	0.97	25	empty
3	401	0.69	0.81	47	empty
4	205	0.56	0.79	27	empty
5	378	0.55	0.74	45	empty

Interfaces

7 interfaces between chains.

C–D · 1666 Å² buried · 15 hydrogen bonds · protein-protein
H–L · 1645 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 862 Å² buried · 21 hydrogen bonds · protein-protein
A–H · 789 Å² buried · 18 hydrogen bonds · protein-protein
H–D · 165 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6LXI · Crystal structure of Z2B3 Fab in complex with influenza virus neuraminidase from A/Brevig… · the same entry in another collection · chain D against D, 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 Q9IGQ6
Elsewhere: RCSB PDB 6LXI · PDBe 6LXI · UniProt Q9IGQ6

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