Research workbench

SARS-cov-2 omicron rbd in complex with omi-6 and covox-150 fabs

Analyse SARS-cov-2 omicron rbd in complex with omi-6 and covox-150 fabs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ZFA
Type: protein
Length: 4,237 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; Omi-6 heavy chain; Omi-6 light chain; Covox-150 heavy chain; Covox-150…
UniProt: P0DTC2
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 11 distinct chains · 8% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C, A	Spike protein S1	protein	195	12% helix, 32% strand	P0DTC2
B	Spike protein S1	protein	194	12% helix, 31% strand	P0DTC2
E, M, J, H	Omi-6 heavy chain	protein	224	9% helix, 54% strand	—
F	Omi-6 light chain	protein	212	6% helix, 50% strand	—
K	Omi-6 light chain	protein	211	6% helix, 50% strand	—
N	Omi-6 light chain	protein	210	6% helix, 49% strand	—
L	Omi-6 light chain	protein	211	6% helix, 49% strand	—
X, S, Q	Covox-150 heavy chain	protein	215	10% helix, 53% strand	—
Y, T, R	Covox-150 light chain	protein	215	5% helix, 48% strand	—
O	Covox-150 heavy chain	protein	214	10% helix, 53% strand	—
P	Covox-150 light chain	protein	214	5% helix, 49% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	864	0.78	0.81	96	empty
2	626	0.71	0.79	62	empty
3	471	0.68	0.79	60	empty
4	170	0.66	0.87	32	empty
5	194	0.66	0.85	32	empty

Interfaces

41 interfaces between chains.

L–H · 1865 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 1812 Å² buried · 15 hydrogen bonds · protein-protein
M–N · 1808 Å² buried · 16 hydrogen bonds · protein-protein
K–J · 1794 Å² buried · 10 hydrogen bonds · protein-protein
S–T · 1777 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide (disulfide).

Compared structures

7ZFA · SARS-CoV-2 Omicron RBD in complex with Omi-6 and COVOX-150 Fabs · 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 P0DTC2
Elsewhere: RCSB PDB 7ZFA · PDBe 7ZFA · UniProt P0DTC2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.