Research workbench

Is FR1 the ANTIBODY'S achillies heel

Analyse Is FR1 the ANTIBODY'S achillies heel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BX5
Type: protein
Length: 1,581 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VD9 vki light-chain
Pockets: 13 · best druggability 0.47

Structure

x-ray diffraction · 2 distinct chains · 1% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, I, J, K, L, M, N, O	VD9 vki light-chain	protein	106	3% helix, 41% strand	—
H	VD9 vki light-chain	protein	97	0% helix, 25% strand	—

Pockets

13 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	217	0.47	0.74	31	empty
2	124	0.43	0.76	20	empty
3	77	0.35	0.76	17	empty
4	86	0.34	0.74	18	empty
5	89	0.34	0.74	25	empty

Interfaces

19 interfaces between chains.

N–O · 647 Å² buried · 15 hydrogen bonds · protein-protein
D–E · 647 Å² buried · 10 hydrogen bonds · protein-protein
J–K · 632 Å² buried · 14 hydrogen bonds · protein-protein
L–M · 623 Å² buried · 13 hydrogen bonds · protein-protein
H–I · 609 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

2BX5 · Is FR1 the antibody's Achillies heel · 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
Elsewhere: RCSB PDB 2BX5 · PDBe 2BX5

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