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Crystal structure of glypican-2 core protein in complex with D3 Fab

Analyse Crystal structure of glypican-2 core protein in complex with D3 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WJL
Type: protein
Length: 1,916 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glypican-2; D3 Fab heavy chain; Vhh domain; D3 Fab light chain
UniProt: Q8N158
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 6 distinct chains · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Glypican-2	protein	419	56% helix, 0% strand	Q8N158
H, F	D3 Fab heavy chain	protein	218	6% helix, 47% strand	—
K	Vhh domain	protein	115	3% helix, 31% strand	—
L, J	D3 Fab light chain	protein	213	5% helix, 49% strand	—
E	Glypican-2	protein	406	59% helix, 0% strand	Q8N158
I	Vhh domain	protein	114	0% helix, 31% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	77	0.74	0.97	16	empty
2	438	0.73	0.83	73	empty
3	1174	0.72	0.76	102	empty
4	344	0.70	0.83	58	empty
5	233	0.68	0.84	23	empty

Interfaces

13 interfaces between chains.

H–L · 1940 Å² buried · 11 hydrogen bonds · protein-protein
F–J · 1908 Å² buried · 12 hydrogen bonds · protein-protein
E–F · 846 Å² buried · 19 hydrogen bonds · protein-protein
G–H · 840 Å² buried · 18 hydrogen bonds · protein-protein
K–L · 621 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide (disulfide).

Compared structures

6WJL · Crystal structure of Glypican-2 core protein in complex with D3 Fab · the same entry in another collection · chain J against J, TM-score 1.00
Q8N158 · AlphaFold monomer V2.0 prediction for glypican-2 (Q8N158) · a predicted model of the same protein · chain E against A, TM-score 0.91

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 Q8N158
Elsewhere: RCSB PDB 6WJL · PDBe 6WJL · UniProt Q8N158

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