MolNFT v1 · #127928 · protein

Principles for computational design of antibodies

5NB5: “Principles for computational design of antibodies”. X-ray diffraction, 12 pockets (best druggability 0.68). MolNFT v1 #127928 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NB5
Type: protein
Length: 864 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Design of antibodies
Pockets: 12 · best druggability 0.68

Structure

x-ray diffraction · 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 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 5NB5 · PDBe 5NB5

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