Research workbench

Crystal structure of N-glycosylated, C-terminally truncated human glypican-1

Analyse Crystal structure of N-glycosylated, C-terminally truncated human glypican-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ACR
Type: protein
Length: 1,592 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glypican-1
UniProt: P35052
Ligands: NAG
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 66% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glypican-1	protein	347	65% helix, 2% strand	P35052
B	Glypican-1	protein	424	67% helix, 2% strand	P35052
C	Glypican-1	protein	393	67% helix, 2% strand	P35052
D	Glypican-1	protein	428	66% helix, 2% strand	P35052

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1167	0.74	0.77	115	empty
2	932	0.73	0.77	82	empty
3	104	0.62	0.88	19	empty
4	324	0.61	0.79	42	empty
5	86	0.60	0.88	19	empty

Interfaces

2 interfaces between chains.

C–D · 570 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 552 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 26 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

4ACR · Crystal structure of N-glycosylated, C-terminally truncated human glypican-1 · the same entry in another collection · chain D against D, TM-score 1.00
P35052 · AlphaFold monomer V2.0 prediction for glypican-1 (P35052) · a predicted model of the same protein · chain D against A, TM-score 0.99

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 P35052
Elsewhere: RCSB PDB 4ACR · PDBe 4ACR · UniProt P35052

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