MolNFT v1 · #180472 · protein

Circulating SARS-cov-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

7L0N · Monoclonal antibody S309 Fab light chain: “Circulating SARS-cov-2 spike N439K variants maintain fitness while evading antibody-mediated immunity”. X-ray diffraction, 8 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.74).…

PDB: 7L0N
Type: protein
Length: 3,304 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Monoclonal antibody S309 Fab light chain; Monoclonal antibody S309 Fab heavy chain…
EC: 3.4.17.23
UniProt: Q9BYF1, P0DTC2
Ligands: NAG, MAN, BMA, FUC, NA, ZN, CL, SO4
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 10 distinct chains · 29% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, D	Monoclonal antibody S309 Fab light chain	protein	213	6% helix, 52% strand	—
A	Monoclonal antibody S309 Fab heavy chain	protein	222	5% helix, 51% strand	—
C	Monoclonal antibody S309 Fab heavy chain	protein	224	7% helix, 52% strand	—
L, N	Monoclonal antibody S304 Fab light chain	protein	213	3% helix, 53% strand	—
H	Monoclonal antibody S304 Fab heavy chain	protein	212	7% helix, 56% strand	—
M	Monoclonal antibody S304 Fab heavy chain	protein	215	6% helix, 57% strand	—
E	Angiotensin-converting enzyme 2 (EC 3.4.17.23)	protein	579	60% helix, 3% strand	Q9BYF1
F	Angiotensin-converting enzyme 2 (EC 3.4.17.23)	protein	596	59% helix, 4% strand	Q9BYF1
R	Spike protein S1	protein	203	14% helix, 29% strand	P0DTC2
S	Spike protein S1	protein	201	14% helix, 30% strand	P0DTC2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains B, A, R, D, C, S, E, H, F, M
MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B, R, D
BMA · beta-D-mannopyranose · sugar · 2 copies
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains B, A, D, C
NA · Sodium ion · metal · 6 copies · chains L, H, R, F
ZN · Zinc ion · metal · 2 copies · chains E, F
CL · Chloride ion · ion · 27 copies · chains B, A, D, C, H, L, N, M, S, E, F, R
SO4 · Sulfate ion · ion · 2 copies · chains L, N
PGE · Triethylene glycol · additive · 2 copies · chains E, S
PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · chains L, H
PG4 · Tetraethylene glycol · additive · chains N

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	992	0.74	0.77	108	PG5
2	522	0.71	0.80	47	empty
3	504	0.71	0.80	48	empty
4	759	0.69	0.76	74	CL
5	796	0.68	0.75	72	empty

Interfaces

17 interfaces between chains.

N–M · 1919 Å² buried · 10 hydrogen bonds · protein-protein
L–H · 1876 Å² buried · 13 hydrogen bonds · protein-protein
B–A · 1690 Å² buried · 13 hydrogen bonds · protein-protein
D–C · 1643 Å² buried · 11 hydrogen bonds · protein-protein
L–N · 1031 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 29 disulfide, 11 glycan (disulfide, N-glycosylation).

Compared structures

7L0N · Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading… · the same entry in another collection · chain R against R, 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 Q9BYF1
Every structure of UniProt P0DTC2
Elsewhere: RCSB PDB 7L0N · PDBe 7L0N · UniProt Q9BYF1 · UniProt P0DTC2

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