MolNFT v1 · #179167 · protein

Mapping neutralizing and immunodominant sites on the SARS-cov-2 spike receptor-binding domain by structure-guided high-resolution serology

7JXC · S2H14 antigen-binding (Fab) fragment: “Mapping neutralizing and immunodominant sites on the SARS-cov-2 spike receptor-binding domain by…”. X-ray diffraction, 6 pockets (best druggability 0.55). MolNFT v1 #179167 on GenesisL1: 3D…

PDB: 7JXC
Type: protein
Length: 428 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: S2H14 antigen-binding (Fab) fragment
Pockets: 6 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	S2H14 antigen-binding (Fab) fragment	protein	215	8% helix, 51% strand	—
L	S2H14 antigen-binding (Fab) fragment	protein	213	7% helix, 50% strand	—

Ligands and binding sites

2PE · Nonaethylene glycol · additive · chains H, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 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	321	0.55	0.75	38	2PE
2	265	0.51	0.75	27	empty
3	115	0.42	0.76	21	empty
4	93	0.41	0.78	27	empty
5	96	0.40	0.77	24	empty

Interfaces

1 interface between chains.

H–L · 1574 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7JXC · Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding… · 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 7JXC · PDBe 7JXC

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