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Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold proteins

Analyse Epitope backbone grafting by computational design for improved presentation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RI0
Type: protein
Length: 311 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: BB_2CX5_001
UniProt: Q5SHN1
Ligands: SO4
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	BB_2CX5_001	protein	156	33% helix, 24% strand	Q5SHN1
B	BB_2CX5_001	protein	155	34% helix, 23% strand	Q5SHN1

Ligands and binding sites

SO4 · Sulfate ion · ion · chains B
GOL · Glycerol · additive · chains A

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

Pockets

3 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	501	0.68	0.79	46	SO4
2	134	0.52	0.80	22	empty
3	156	0.49	0.77	25	empty

Interfaces

1 interface between chains.

A–B · 329 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

3RI0 · Epitope backbone grafting by computational design for improved presentation of linear… · 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 Q5SHN1
Elsewhere: RCSB PDB 3RI0 · PDBe 3RI0 · UniProt Q5SHN1

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