Research workbench

Dual epitope targeting by anti-DR5 antibodies

Analyse Dual epitope targeting by anti-DR5 antibodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T3J
Type: protein
Length: 1,942 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IGG1-HDR5-01-heavy chain; IGG1-HDR5-01-light chain; IGG1-HDR5-05-heavy chain…
UniProt: O14763
Pockets: 20 · best druggability 0.59

Structure

x-ray diffraction · 8 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, F	IGG1-HDR5-01-heavy chain	protein	219	5% helix, 51% strand	—
B	IGG1-HDR5-01-light chain	protein	212	7% helix, 50% strand	—
C	IGG1-HDR5-05-heavy chain	protein	219	5% helix, 53% strand	—
D, I	IGG1-HDR5-05-light chain	protein	210	7% helix, 50% strand	—
E	Tumor necrosis factor receptor superfamily member 10B	protein	112	0% helix, 35% strand	O14763
G	IGG1-HDR5-01-light chain	protein	213	7% helix, 50% strand	—
H	IGG1-HDR5-05-heavy chain	protein	218	6% helix, 53% strand	—
J	Tumor necrosis factor receptor superfamily member 10B	protein	110	0% helix, 34% strand	O14763

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	322	0.59	0.77	42	empty
2	391	0.56	0.74	53	empty
3	358	0.55	0.74	49	empty
4	295	0.54	0.75	45	empty
5	67	0.54	0.87	25	empty

Interfaces

12 interfaces between chains.

H–I · 2029 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1975 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1969 Å² buried · 18 hydrogen bonds · protein-protein
F–G · 1928 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 587 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 29 disulfide, 2 modified (disulfide, phosphorylation).

Compared structures

6T3J · Dual Epitope Targeting by Anti-DR5 Antibodies · the same entry in another collection · chain J against J, TM-score 1.00
O14763 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain J against A, TM-score 0.92

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 O14763
Elsewhere: RCSB PDB 6T3J · PDBe 6T3J · UniProt O14763

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.