MolNFT v1 · #127814 · protein

Computationally designed functional antibody

5N7W · Antibody fragment heavy chain: “Computationally designed functional antibody”. X-ray diffraction, 11 pockets (best druggability 0.62). MolNFT v1 #127814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5N7W
Type: protein
Length: 1,070 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody fragment heavy chain; Antibody fragment light chain; Interleukin-17A
UniProt: Q16552
Pockets: 11 · best druggability 0.62

Structure

x-ray diffraction · 6 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antibody fragment heavy chain	protein	220	7% helix, 50% strand	—
B	Antibody fragment light chain	protein	210	6% helix, 51% strand	—
H	Antibody fragment heavy chain	protein	216	7% helix, 51% strand	—
L	Antibody fragment light chain	protein	211	6% helix, 52% strand	—
X	Interleukin-17A	protein	108	4% helix, 55% strand	Q16552
Y	Interleukin-17A	protein	105	4% helix, 56% strand	Q16552

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	174	0.62	0.84	29	empty
2	210	0.52	0.77	37	empty
3	179	0.48	0.76	32	empty
4	213	0.47	0.74	35	empty
5	164	0.44	0.74	30	empty

Interfaces

11 interfaces between chains.

X–Y · 2419 Å² buried · 35 hydrogen bonds · protein-protein
H–L · 1758 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1664 Å² buried · 16 hydrogen bonds · protein-protein
B–Y · 679 Å² buried · 8 hydrogen bonds · protein-protein
L–X · 609 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

5N7W · Computationally designed functional antibody · the same entry in another collection · chain Y against Y, TM-score 1.00
Q16552 · AlphaFold monomer V2.0 prediction for interleukin-17A (Q16552) · a predicted model of the same protein · chain Y against A, TM-score 0.84

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q16552
Elsewhere: RCSB PDB 5N7W · PDBe 5N7W · UniProt Q16552

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