MolNFT v1 · #77556 · protein

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

3RIJ · SC_2CX5: “Epitope backbone grafting by computational design for improved presentation of linear epitopes on scaffold…”. X-ray diffraction, 8 pockets (best druggability 0.58). MolNFT v1 #77556 on GenesisL1: 3D structure, binding…

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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