Research workbench

Crystal structure of human nectin-1 full ectodomain (D1-D3)

Analyse Crystal structure of human nectin-1 full ectodomain (D1-D3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FMF
Type: protein
Length: 1,204 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poliovirus receptor-related protein 1
UniProt: Q15223
Ligands: NAG
Pockets: 5 · best druggability 0.31

Structure

x-ray diffraction · 3 distinct chains · 2% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Poliovirus receptor-related protein 1	protein	302	2% helix, 56% strand	Q15223
B	Poliovirus receptor-related protein 1	protein	299	2% helix, 59% strand	Q15223
C	Poliovirus receptor-related protein 1	protein	301	2% helix, 57% strand	Q15223

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
FMT · Formic acid · additive · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	86	0.31	0.73	22	empty
2	64	0.31	0.75	12	empty
3	64	0.28	0.73	17	empty
4	65	0.28	0.73	17	empty
5	58	0.26	0.73	15	empty

Interfaces

3 interfaces between chains.

C–D · 871 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 854 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 600 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4FMF · Crystal structure of human nectin-1 full ectodomain (D1-D3) · the same entry in another collection · chain A against A, TM-score 1.00
Q15223 · AlphaFold monomer V2.0 prediction for nectin-1 (Q15223) · a predicted model of the same protein · chain C against A, TM-score 0.97

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 Q15223
Elsewhere: RCSB PDB 4FMF · PDBe 4FMF · UniProt Q15223

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