MolNFT v1 · #100835 · protein

Crystal structure of a computationally designed rsv-presenting epitope scaffold and its elicited antibody 17HD9

4N9G · Antibody 17HD9, heavy chain: “Crystal structure of a computationally designed rsv-presenting epitope scaffold and its elicited antibody…”. X-ray diffraction, 20 pockets (best druggability 0.72). MolNFT v1 #100835 on GenesisL1: 3D…

PDB: 4N9G
Type: protein
Length: 1,889 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody 17HD9, heavy chain; Antibody 17HD9, light chain; Epitope scaffold…
Pockets: 20 · best druggability 0.72

Structure

x-ray diffraction · 8 distinct chains · 14% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antibody 17HD9, heavy chain	protein	224	7% helix, 51% strand	—
B, F, L, N	Antibody 17HD9, light chain	protein	214	6% helix, 50% strand	—
C	Epitope scaffold RSV_1ISEA_FFL_001_C	protein	35	80% helix, 0% strand	—
D	Epitope scaffold RSV_1ISEA_FFL_001_C	protein	35	83% helix, 0% strand	—
E	Antibody 17HD9, heavy chain	protein	223	7% helix, 51% strand	—
H	Antibody 17HD9, heavy chain	protein	221	9% helix, 51% strand	—
M	Antibody 17HD9, heavy chain	protein	223	8% helix, 51% strand	—
Y, Z	Epitope scaffold RSV_1ISEA_FFL_001_C	protein	36	81% helix, 0% strand	—

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	735	0.72	0.78	92	empty
2	578	0.65	0.76	38	empty
3	259	0.58	0.78	37	empty
4	304	0.57	0.77	50	empty
5	389	0.55	0.74	71	empty

Interfaces

25 interfaces between chains.

E–F · 1890 Å² buried · 21 hydrogen bonds · protein-protein
M–N · 1889 Å² buried · 26 hydrogen bonds · protein-protein
A–B · 1868 Å² buried · 20 hydrogen bonds · protein-protein
H–L · 1847 Å² buried · 25 hydrogen bonds · protein-protein
C–Z · 703 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 disulfide (disulfide).

Compared structures

4N9G · Crystal Structure of a Computationally Designed RSV-Presenting Epitope Scaffold And Its… · 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 4N9G · PDBe 4N9G

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.