MolNFT v1 · #85462 · protein

Crystal structure of full-length N-glycosylated human glypican-1

4AD7: “Crystal structure of full-length N-glycosylated human glypican-1”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.75). MolNFT v1 #85462 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4AD7
Type: protein
Length: 1,597 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 0.75

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glypican-1	protein	358	66% helix, 3% strand	P35052
B	Glypican-1	protein	426	67% helix, 2% strand	P35052
C	Glypican-1	protein	385	66% 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	1114	0.75	0.78	102	empty
2	717	0.69	0.77	69	empty
3	201	0.64	0.83	25	empty
4	280	0.63	0.81	38	empty
5	80	0.61	0.89	16	empty

Interfaces

2 interfaces between chains.

C–D · 621 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 578 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

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

Compared structures

4AD7 · Crystal structure of full-length N-glycosylated 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 B 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 4AD7 · PDBe 4AD7 · UniProt P35052

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