MolNFT v1 · #190357 · protein

S protein of delta variant in complex with ZWC6

7WWM · Spike glycoprotein: “S protein of delta variant in complex with ZWC6”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #190357 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7WWM
Type: protein
Length: 3,655 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; Heavy chain of ZWC6
UniProt: P0DTC2
Ligands: NAG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 4 distinct chains · 17% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	994	20% helix, 30% strand	P0DTC2
B, C	Spike glycoprotein	protein	993	19% helix, 30% strand	P0DTC2
H, I, J	Heavy chain of ZWC6	protein	120	0% helix, 42% strand	—
L, M, N	Heavy chain of ZWC6	protein	105	0% helix, 36% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 71 copies · chains A, H, B, I, C, J

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

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	1121	0.83	0.84	132	empty
2	604	0.83	0.88	90	empty
3	637	0.83	0.87	68	empty
4	1077	0.79	0.81	81	empty
5	1177	0.77	0.79	88	empty

Interfaces

14 interfaces between chains.

B–C · 4377 Å² buried · 32 hydrogen bonds · protein-protein
A–C · 4245 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 3933 Å² buried · 24 hydrogen bonds · protein-protein
J–N · 861 Å² buried · 7 hydrogen bonds · protein-protein
H–L · 856 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 glycan, 45 disulfide (N-glycosylation, disulfide).

Compared structures

7WWM · S protein of Delta variant in complex with ZWC6 · 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
Elsewhere: RCSB PDB 7WWM · PDBe 7WWM · UniProt P0DTC2

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