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Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C119

Analyse Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7K8W
Type: protein
Length: 3,403 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; C119 Fab heavy chain; C119 Fab light chain
UniProt: P0DTC2
Ligands: NAG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 5 distinct chains · 21% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	990	23% helix, 31% strand	P0DTC2
B	Spike glycoprotein	protein	949	23% helix, 31% strand	P0DTC2
G	Spike glycoprotein	protein	990	22% helix, 32% strand	P0DTC2
H, N	C119 Fab heavy chain	protein	126	5% helix, 45% strand	—
L, S	C119 Fab light chain	protein	111	7% helix, 46% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, G, B

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	1010	0.83	0.84	110	empty
2	506	0.83	0.89	61	empty
3	874	0.81	0.83	85	empty
4	1066	0.79	0.81	122	empty
5	695	0.79	0.84	69	empty

Interfaces

12 interfaces between chains.

A–G · 4644 Å² buried · 43 hydrogen bonds · protein-protein
A–B · 4520 Å² buried · 34 hydrogen bonds · protein-protein
B–G · 4044 Å² buried · 32 hydrogen bonds · protein-protein
H–L · 762 Å² buried · 5 hydrogen bonds · protein-protein
N–S · 711 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 47 glycan, 42 disulfide (N-glycosylation, disulfide).

Compared structures

7K8W · Structure of the SARS-CoV-2 S 2P trimer in complex with the human neutralizing antibody… · 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 7K8W · PDBe 7K8W · UniProt P0DTC2

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