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SARS-cov-2 U1S2Q all down rbd state spike protein trimer - asymmetric refinement

Analyse SARS-cov-2 U1S2Q all down rbd state spike protein trimer - asymmetric refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7M0J
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 0.86

Structure

electron microscopy · 1 distinct chain · 23% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Spike glycoprotein	protein	972	23% helix, 32% 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	802	0.86	0.89	106	empty
2	923	0.82	0.83	114	empty
3	969	0.82	0.83	104	empty
4	381	0.81	0.90	51	empty
5	487	0.78	0.86	47	empty

Interfaces

3 interfaces between chains.

B–C · 5285 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 5278 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 5268 Å² buried · 43 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide (disulfide).

Compared structures

7M0J · SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer - asymmetric refinement · 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 7M0J · PDBe 7M0J · UniProt P0DTC2

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