MolNFT v1 · #188605 · protein

Crystal structure of C13B8 Fab in complex with SARS-cov-2 S fusion peptide

7U09 · Heavy chain Fab C13B8: “Crystal structure of C13B8 Fab in complex with SARS-cov-2 S fusion peptide”. X-ray diffraction, 4 pockets (best druggability 0.55). MolNFT v1 #188605 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7U09
Type: protein
Length: 446 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain Fab C13B8; Light chain Fab C13B8; SARS-cov-2 S fusion peptide
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Heavy chain Fab C13B8	protein	227	5% helix, 49% strand	—
L	Light chain Fab C13B8	protein	208	7% helix, 50% strand	—
A	SARS-cov-2 S fusion peptide	protein	11	45% helix, 9% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	425	0.55	0.73	59	empty
2	74	0.39	0.78	23	empty
3	60	0.30	0.75	19	empty
4	75	0.30	0.73	22	empty

Interfaces

3 interfaces between chains.

H–L · 1792 Å² buried · 15 hydrogen bonds · protein-protein
L–A · 450 Å² buried · 8 hydrogen bonds · protein-protein
H–A · 301 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7U09 · Crystal Structure of C13B8 Fab in complex with SARS-CoV-2 S fusion peptide · the same entry in another collection · chain H against H, 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
Elsewhere: RCSB PDB 7U09 · PDBe 7U09

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