MolNFT v1 · #181866 · protein

SARS-cov-2 S-ntd + Fab CM25

7M8J · Spike protein S1: “SARS-cov-2 S-ntd + Fab CM25”. Electron microscopy, 7 pockets (best druggability 0.54). MolNFT v1 #181866 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7M8J
Type: protein
Length: 453 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; CM25 Fab - heavy chain; CM25 Fab - light chain
UniProt: P0DTC2
Pockets: 7 · best druggability 0.54

Structure

electron microscopy · 3 distinct chains · 3% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	224	1% helix, 40% strand	P0DTC2
H	CM25 Fab - heavy chain	protein	120	5% helix, 50% strand	—
L	CM25 Fab - light chain	protein	109	5% helix, 47% strand	—

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.54	0.89	22	empty
2	76	0.53	0.85	17	empty
3	88	0.47	0.81	23	empty
4	71	0.41	0.79	17	empty
5	91	0.40	0.77	15	empty

Interfaces

3 interfaces between chains.

H–L · 862 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 751 Å² buried · 3 hydrogen bonds · protein-protein
A–L · 101 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7M8J · SARS-CoV-2 S-NTD + Fab CM25 · 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 7M8J · PDBe 7M8J · UniProt P0DTC2

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