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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: 3RIJ
Type: protein
Length: 620 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SC_2CX5
UniProt: Q5SHN1
Pockets: 8 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 30% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	SC_2CX5	protein	157	34% helix, 25% strand	Q5SHN1
B	SC_2CX5	protein	156	33% helix, 24% strand	Q5SHN1
C	SC_2CX5	protein	150	24% helix, 25% strand	Q5SHN1

Ligands and binding sites

GOL · Glycerol · additive · chains C

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	279	0.58	0.78	27	empty
2	187	0.56	0.80	29	empty
3	193	0.55	0.79	28	empty
4	251	0.53	0.76	28	empty
5	159	0.50	0.78	27	empty

Interfaces

4 interfaces between chains.

A–D · 782 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 243 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 218 Å² buried · 1 hydrogen bond · protein-protein
B–D · 204 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

3RIJ · 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 3RIJ · PDBe 3RIJ · UniProt Q5SHN1

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