Research workbench

SARS-cov-2 omicron variant spike in complex with three human neutralizing antibodies

Analyse SARS-cov-2 omicron variant spike in complex with three human neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WI0
Type: protein
Length: 886 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; XMA04 heavy chain variable domain; XMA01 heavy chain variable domain…
UniProt: P0DTC2, A0A5C2G4I7, A0A5C2GTV1, A0A5C2GVU3
Ligands: NAG
Pockets: 10 · best druggability 0.73

Structure

electron microscopy · 7 distinct chains · 2% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	194	6% helix, 28% strand	P0DTC2
B	XMA04 heavy chain variable domain	protein	123	0% helix, 35% strand	—
C	XMA01 heavy chain variable domain	protein	122	2% helix, 40% strand	—
D	Igl C4029_LIGHT_IGKV1-39_IGKJ2	protein	107	0% helix, 50% strand	A0A5C2G4I7
E	Ig C934_LIGHT_IGKV1-5_IGKJ1	protein	107	0% helix, 41% strand	A0A5C2GTV1
H	XMA09 heavy chain variable domain	protein	123	0% helix, 39% strand	—
L	Ig C1437_LIGHT_IGLV1-40_IGLJ1	protein	110	0% helix, 43% strand	A0A5C2GVU3

Ligands and binding sites

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

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

Pockets

10 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	842	0.73	0.78	88	empty
2	351	0.60	0.77	36	empty
3	420	0.60	0.76	51	empty
4	121	0.49	0.80	27	empty
5	124	0.41	0.76	27	empty

Interfaces

12 interfaces between chains.

C–E · 951 Å² buried · 6 hydrogen bonds · protein-protein
H–L · 898 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 859 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 828 Å² buried · 8 hydrogen bonds · protein-protein
A–H · 647 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7WI0 · SARS-CoV-2 Omicron variant spike in complex with three human neutralizing antibodies · 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 P0DTC2
Every structure of UniProt A0A5C2G4I7
Every structure of UniProt A0A5C2GTV1
Every structure of UniProt A0A5C2GVU3
Elsewhere: RCSB PDB 7WI0 · PDBe 7WI0 · UniProt P0DTC2 · UniProt A0A5C2G4I7 · UniProt A0A5C2GTV1 · UniProt A0A5C2GVU3

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