MolNFT v1 · #140400 · protein

Structure of the belimumab Fab fragment

5Y9K · Belimumab light chain: “Structure of the belimumab Fab fragment”. X-ray diffraction, 3 pockets (best druggability 0.63). MolNFT v1 #140400 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5Y9K
Type: protein
Length: 425 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Belimumab light chain; Belimumab heavy chain
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Belimumab light chain	protein	209	9% helix, 51% strand	—
H	Belimumab heavy chain	protein	216	6% helix, 51% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	618	0.63	0.75	65	empty
2	88	0.49	0.83	21	empty
3	57	0.34	0.78	18	empty

Interfaces

1 interface between chains.

L–H · 1763 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5Y9K · Structure of the belimumab Fab fragment · the same entry in another collection · chain L against L, 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
Elsewhere: RCSB PDB 5Y9K · PDBe 5Y9K

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