MolNFT v1 · #187878 · protein

SARS-cov-2 S-rbd + Fab 54042-4

7T01 · Spike protein S1: “SARS-cov-2 S-rbd + Fab 54042-4”. Electron microscopy, 2 pockets (best druggability 0.41). MolNFT v1 #187878 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7T01
Type: protein
Length: 428 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike protein S1; 54042-4 Fab - heavy chain; 54042-4 Fab - light chain
UniProt: P0DTC2
Pockets: 2 · best druggability 0.41

Structure

electron microscopy · 3 distinct chains · 10% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike protein S1	protein	201	15% helix, 28% strand	P0DTC2
H	54042-4 Fab - heavy chain	protein	120	8% helix, 44% strand	—
L	54042-4 Fab - light chain	protein	107	3% helix, 47% strand	—

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.41	0.78	20	empty
2	61	0.28	0.74	23	empty

Interfaces

3 interfaces between chains.

H–L · 919 Å² buried · 8 hydrogen bonds · protein-protein
A–H · 411 Å² buried · 6 hydrogen bonds · protein-protein
A–L · 251 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

7T01 · SARS-CoV-2 S-RBD + Fab 54042-4 · 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 7T01 · PDBe 7T01 · UniProt P0DTC2

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