MolNFT v1 · #169152 · protein

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

6X2C · Spike glycoprotein: “SARS-cov-2 U1S2Q all down rbd state spike protein trimer”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #169152 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6X2C
Type: protein
Length: 2,913 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: P0DTC2
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 24% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Spike glycoprotein	protein	971	24% 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	597	0.85	0.90	74	empty
2	1006	0.84	0.86	125	empty
3	748	0.84	0.87	76	empty
4	907	0.84	0.85	93	empty
5	930	0.83	0.84	84	empty

Interfaces

3 interfaces between chains.

B–C · 5213 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 5202 Å² buried · 43 hydrogen bonds · protein-protein
A–C · 5199 Å² buried · 42 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 36 disulfide (disulfide).

Compared structures

6X2C · SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer · 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 6X2C · PDBe 6X2C · UniProt P0DTC2

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