Research workbench

Baff in complex with belimumab

Analyse Baff in complex with belimumab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y9J
Type: protein
Length: 572 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Belibumab light chain; Belimumab heavy chain; Tumor necrosis factor ligand superfamily…
UniProt: Q9Y275
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Belibumab light chain	protein	210	9% helix, 50% strand	—
H	Belimumab heavy chain	protein	218	7% helix, 48% strand	—
A	Tumor necrosis factor ligand superfamily member 13B	protein	144	0% helix, 56% strand	Q9Y275

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	123	0.76	0.95	30	empty
2	90	0.64	0.90	25	empty
3	469	0.57	0.73	55	empty
4	100	0.41	0.77	17	empty
5	64	0.34	0.77	18	empty

Interfaces

3 interfaces between chains.

L–H · 1622 Å² buried · 10 hydrogen bonds · protein-protein
H–A · 560 Å² buried · 10 hydrogen bonds · protein-protein
L–A · 439 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5Y9J · BAFF in complex with belimumab · the same entry in another collection · chain L against L, TM-score 1.00
Q9Y275 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 13B… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9Y275
Elsewhere: RCSB PDB 5Y9J · PDBe 5Y9J · UniProt Q9Y275

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