Research workbench

SARS-cov-2 omicron rbd in complex with omi-3 and EY6A fabs

Analyse SARS-cov-2 omicron rbd in complex with omi-3 and EY6A fabs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ZF3
Type: protein
Length: 1,055 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: EY6A heavy chain; EY6A light chain; Omi-3 heavy chain; Omi-3 light chain; Spike protein S1
UniProt: P0DTC2
Pockets: 13 · best druggability 0.71

Structure

x-ray diffraction · 5 distinct chains · 6% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	EY6A heavy chain	protein	217	6% helix, 51% strand	—
L	EY6A light chain	protein	214	6% helix, 50% strand	—
A	Omi-3 heavy chain	protein	214	1% helix, 52% strand	—
B	Omi-3 light chain	protein	215	7% helix, 50% strand	—
E	Spike protein S1	protein	195	12% helix, 31% strand	P0DTC2

Ligands and binding sites

GOL · Glycerol · additive · 4 copies · chains L, H, A, B, E
IPA · Isopropyl alcohol · additive · 2 copies · chains A

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

Pockets

13 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	58	0.71	0.98	24	empty
2	538	0.60	0.74	62	IPA
3	300	0.51	0.73	42	empty
4	55	0.47	0.85	17	empty
5	180	0.46	0.75	33	empty

Interfaces

6 interfaces between chains.

H–L · 1902 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1733 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 887 Å² buried · 12 hydrogen bonds · protein-protein
H–E · 753 Å² buried · 12 hydrogen bonds · protein-protein
L–E · 472 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 1 covalent (disulfide, additive adduct).

Compared structures

7ZF3 · SARS-CoV-2 Omicron RBD in complex with Omi-3 and EY6A Fabs · the same entry in another collection · chain H against H, 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 7ZF3 · PDBe 7ZF3 · UniProt P0DTC2

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