MolNFT v1 · #114806 · protein

Crystal structure of a generation 3 influenza hemagglutinin stabilized stem complexed with the broadly neutralizing antibody C179

5C0R · Hemagglutinin, envelope glycoprotein, fibritin fusion…: “Crystal structure of a generation 3 influenza hemagglutinin stabilized stem complexed with the broadly…”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability…

PDB: 5C0R
Type: protein
Length: 706 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hemagglutinin, envelope glycoprotein, fibritin fusion protein; C179 Fab light chain; C179…
UniProt: Q6WG00, P04578, D9IEJ2
Ligands: NAG
Pockets: 7 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hemagglutinin, envelope glycoprotein, fibritin fusion protein	protein	270	50% helix, 17% strand	Q6WG00, P04578, D9IEJ2
L	C179 Fab light chain	protein	214	4% helix, 50% strand	—
H	C179 Fab heavy chain	protein	222	4% helix, 49% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	250	0.57	0.78	33	empty
2	282	0.52	0.75	37	empty
3	120	0.51	0.80	18	empty
4	191	0.49	0.76	22	empty
5	252	0.48	0.74	48	empty

Interfaces

3 interfaces between chains.

L–H · 1983 Å² buried · 21 hydrogen bonds · protein-protein
A–H · 589 Å² buried · 2 hydrogen bonds · protein-protein
A–L · 384 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5C0R · Crystal Structure of a Generation 3 Influenza Hemagglutinin Stabilized Stem Complexed… · 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 Q6WG00
Every structure of UniProt P04578
Every structure of UniProt D9IEJ2
Elsewhere: RCSB PDB 5C0R · PDBe 5C0R · UniProt Q6WG00 · UniProt P04578 · UniProt D9IEJ2

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