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Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, C002 (state 1)

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PDB: 7K8S
Type: protein
Length: 3,708 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; C002 Fab heavy chain; C002 Fab light chain
UniProt: P0DTC2
Ligands: NAG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 3 distinct chains · 19% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Spike glycoprotein	protein	1004	23% helix, 30% strand	P0DTC2
H, M, O	C002 Fab heavy chain	protein	125	7% helix, 48% strand	—
L, N, P	C002 Fab light chain	protein	107	0% helix, 46% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 copies · chains A, B, C

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	590	0.83	0.89	78	empty
2	804	0.82	0.85	83	empty
3	888	0.82	0.84	82	empty
4	1129	0.82	0.83	116	empty
5	783	0.81	0.84	74	empty

Interfaces

16 interfaces between chains.

A–C · 4839 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 4622 Å² buried · 49 hydrogen bonds · protein-protein
B–C · 4600 Å² buried · 35 hydrogen bonds · protein-protein
M–N · 836 Å² buried · 12 hydrogen bonds · protein-protein
O–P · 810 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 glycan, 39 disulfide (N-glycosylation, disulfide).

Compared structures

7K8S · 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 7K8S · PDBe 7K8S · UniProt P0DTC2

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