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Principles for computational design of antibodies

Analyse Principles for computational design of antibodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5NB5
Type: protein
Length: 864 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3
Source: synthetic construct
Molecule: design of antibodies
Pockets: 12 · best druggability 0.68

Structure

x-ray diffraction · resolution 3 · 2 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	design of antibodies	protein	218	6% helix, 50% strand	—
H, I	design of antibodies	protein	214	6% helix, 50% strand	—

Pockets

12 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	838	0.68	0.74	95	empty
2	602	0.62	0.74	59	empty
3	261	0.55	0.77	38	empty
4	151	0.54	0.81	24	empty
5	241	0.54	0.77	39	empty

Interfaces

4 interfaces between chains.

M–I · 1841 Å² buried · 15 hydrogen bonds · protein-protein
L–H · 1823 Å² buried · 13 hydrogen bonds · protein-protein
L–M · 394 Å² buried · 3 hydrogen bonds · protein-protein
H–M · 37 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

5NB5 · Principles for computational design of antibodies · the same entry in another collection · chain H against H, 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 5NB5 · PDBe 5NB5

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