MolNFT v1 · #191018 · protein

SARS-cov-2 omicron BA.2 rbd in complex with covox-150 Fab (P21)

7ZF9 · Covox-150 heavy chain: “SARS-cov-2 omicron BA.2 rbd in complex with covox-150 Fab (P21)”. X-ray diffraction, 1 ligand (NAG), 14 pockets (best druggability 0.56). MolNFT v1 #191018 on GenesisL1: 3D structure, binding sites and…

PDB: 7ZF9
Type: protein
Length: 1,256 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Covox-150 heavy chain; Covox-150 light chain; Spike protein S1
UniProt: P0DTC2
Ligands: NAG
Pockets: 14 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Covox-150 heavy chain	protein	220	10% helix, 52% strand	—
L, B	Covox-150 light chain	protein	215	5% helix, 50% strand	—
E, C	Spike protein S1	protein	195	15% helix, 30% strand	P0DTC2
A	Covox-150 heavy chain	protein	216	10% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, C

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	224	0.56	0.78	50	empty
2	241	0.55	0.77	36	empty
3	364	0.55	0.74	45	empty
4	191	0.52	0.78	35	empty
5	108	0.50	0.81	25	empty

Interfaces

9 interfaces between chains.

H–L · 1906 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 1791 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 801 Å² buried · 19 hydrogen bonds · protein-protein
H–E · 795 Å² buried · 19 hydrogen bonds · protein-protein
H–B · 413 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7ZF9 · SARS-CoV-2 Omicron BA.2 RBD in complex with COVOX-150 Fab (P21) · 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 7ZF9 · PDBe 7ZF9 · UniProt P0DTC2

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