MolNFT v1 · #190123 · protein

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

7WHZ · Spike protein S1: “SARS-cov-2 spike protein in complex with three human neutralizing antibodies”. Electron microscopy, 1 ligand (NAG), 9 pockets (best druggability 0.72). MolNFT v1 #190123 on GenesisL1: 3D structure, binding sites…

PDB: 7WHZ
Type: protein
Length: 887 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: 9 · best druggability 0.72

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	194	5% helix, 24% strand	P0DTC2
B	XMA04 heavy chain variable domain	protein	124	0% helix, 38% strand	—
C	XMA01 heavy chain variable domain	protein	122	5% helix, 49% strand	—
D	Igl C4029_LIGHT_IGKV1-39_IGKJ2	protein	107	0% helix, 51% strand	A0A5C2G4I7
E	Ig C934_LIGHT_IGKV1-5_IGKJ1	protein	107	0% helix, 37% strand	A0A5C2GTV1
H	XMA09 heavy chain variable domain	protein	123	0% helix, 35% strand	—
L	Ig C1437_LIGHT_IGLV1-40_IGLJ1	protein	110	0% helix, 37% 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

9 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	738	0.72	0.79	64	empty
2	466	0.62	0.76	46	empty
3	314	0.61	0.78	32	empty
4	134	0.44	0.77	25	empty
5	153	0.41	0.74	32	empty

Interfaces

12 interfaces between chains.

C–E · 919 Å² buried · 7 hydrogen bonds · protein-protein
H–L · 862 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 807 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 779 Å² buried · 10 hydrogen bonds · protein-protein
A–H · 661 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7WHZ · SARS-CoV-2 spike protein 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 7WHZ · PDBe 7WHZ · UniProt P0DTC2 · UniProt A0A5C2G4I7 · UniProt A0A5C2GTV1 · UniProt A0A5C2GVU3

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