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Association of two complexes of largely structurally disordered spike ectodomain with bound EY6A Fab

Analyse Association of two complexes of largely structurally disordered spike… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZFO
Type: protein
Length: 1,252 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; EY6A heavy chain; EY6A light chain
UniProt: P0DTC2
Ligands: NAG
Pockets: 13 · best druggability 0.75

Structure

electron microscopy · 3 distinct chains · 7% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, A	Spike protein S1	protein	194	11% helix, 29% strand	P0DTC2
H, B	EY6A heavy chain	protein	218	3% helix, 49% strand	—
L, C	EY6A light chain	protein	214	7% helix, 55% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains E, 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, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	708	0.75	0.80	71	empty
2	817	0.72	0.77	56	empty
3	414	0.58	0.75	54	empty
4	312	0.58	0.77	53	empty
5	426	0.58	0.74	50	empty

Interfaces

7 interfaces between chains.

B–C · 1983 Å² buried · 10 hydrogen bonds · protein-protein
H–L · 1981 Å² buried · 10 hydrogen bonds · protein-protein
E–H · 624 Å² buried · 7 hydrogen bonds · protein-protein
E–A · 618 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 606 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6ZFO · Association of two complexes of largely structurally disordered Spike ectodomain with… · 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 6ZFO · PDBe 6ZFO · UniProt P0DTC2

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