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Bispecific digoxigenin binding antibodies for targeted payload delivery

Analyse Bispecific digoxigenin binding antibodies for targeted payload delivery in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3RA7
Type: protein
Length: 872 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment, light chain; Fab fragment, heavy chain
Ligands: DOG
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Fab fragment, light chain	protein	211	6% helix, 51% strand	—
H, I	Fab fragment, heavy chain	protein	225	6% helix, 48% strand	—

Ligands and binding sites

DOG · Digoxigenin · ligand · 2 copies · chains L, H, M, I

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 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	1050	0.76	0.78	108	empty
2	189	0.61	0.82	26	DOG
3	210	0.60	0.81	25	DOG
4	259	0.57	0.78	45	empty
5	176	0.51	0.78	29	empty

Interfaces

6 interfaces between chains.

M–I · 1763 Å² buried · 14 hydrogen bonds · protein-protein
L–H · 1762 Å² buried · 12 hydrogen bonds · protein-protein
H–I · 651 Å² buried · 12 hydrogen bonds · protein-protein
L–M · 243 Å² buried · 1 hydrogen bond · protein-protein
H–M · 162 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3RA7 · Bispecific digoxigenin binding antibodies for targeted payload delivery · 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 3RA7 · PDBe 3RA7

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