MolNFT v1 · #182642 · protein

SARS-cov-2 receptor binding domain bound to Fab wcsl 119

7MZH · Spike protein S1: “SARS-cov-2 receptor binding domain bound to Fab wcsl 119”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 14 pockets (best druggability 0.72). MolNFT v1 #182642 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7MZH
Type: protein
Length: 1,256 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; Wcsl 119 heavy chain; Wcsl 119 light chain
UniProt: P0DTC2
Ligands: NAG, BMA, MAN, FUC
Pockets: 14 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 11% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Spike protein S1	protein	197	19% helix, 30% strand	P0DTC2
H	Wcsl 119 heavy chain	protein	215	8% helix, 51% strand	—
L	Wcsl 119 light chain	protein	214	7% helix, 50% strand	—
A	Spike protein S1	protein	198	19% helix, 30% strand	P0DTC2
B	Wcsl 119 heavy chain	protein	216	8% helix, 50% strand	—
C	Wcsl 119 light chain	protein	216	6% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, A
BMA · beta-D-mannopyranose · sugar · 2 copies
MAN · alpha-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains A

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	802	0.72	0.78	88	empty
2	679	0.65	0.75	63	empty
3	599	0.64	0.75	59	empty
4	305	0.57	0.76	27	empty
5	290	0.55	0.76	35	empty

Interfaces

9 interfaces between chains.

B–C · 1644 Å² buried · 14 hydrogen bonds · protein-protein
H–L · 1616 Å² buried · 12 hydrogen bonds · protein-protein
E–L · 543 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 542 Å² buried · 5 hydrogen bonds · protein-protein
E–H · 365 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 17 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

7MZH · SARS-CoV-2 receptor binding domain bound to Fab WCSL 119 · the same entry in another collection · chain E against E, 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 7MZH · PDBe 7MZH · UniProt P0DTC2

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