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Down-state locked RS2D SARS-cov-2 spike ectodomain in the rbd-down conformation, state 2

Analyse Down-state locked RS2D SARS-cov-2 spike ectodomain in the rbd-down… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TLB
Type: protein
Length: 2,916 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: P0DTC2
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 1 distinct chain · 23% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Spike glycoprotein	protein	972	23% helix, 35% strand	P0DTC2

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	667	0.84	0.88	83	empty
2	666	0.82	0.87	95	empty
3	541	0.81	0.88	65	empty
4	824	0.81	0.84	91	empty
5	819	0.78	0.81	90	empty

Interfaces

3 interfaces between chains.

A–B · 5507 Å² buried · 49 hydrogen bonds · protein-protein
A–C · 5150 Å² buried · 42 hydrogen bonds · protein-protein
B–C · 5094 Å² buried · 43 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 39 disulfide (disulfide).

Compared structures

7TLB · Down-state locked rS2d SARS-CoV-2 spike ectodomain in the RBD-down conformation, State 2 · 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 7TLB · PDBe 7TLB · UniProt P0DTC2

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