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Crystal structure of LRP6-E1E2

Analyse Crystal structure of LRP6-E1E2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S94
Type: protein
Length: 1,170 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Low-density lipoprotein receptor-related protein 6
UniProt: O75581
Ligands: NAG
Pockets: 13 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 2% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Low-density lipoprotein receptor-related protein 6	protein	587	2% helix, 46% strand	O75581
B	Low-density lipoprotein receptor-related protein 6	protein	583	1% helix, 44% strand	O75581

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A

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

Pockets

13 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	282	0.82	0.93	50	empty
2	304	0.80	0.91	47	empty
3	78	0.76	0.98	18	empty
4	77	0.74	0.98	18	empty
5	465	0.62	0.76	54	empty

Interfaces

1 interface between chains.

A–B · 54 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

3S94 · Crystal structure of LRP6-E1E2 · the same entry in another collection · chain A against A, TM-score 1.00
O75581 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor-related protein 6… · a predicted model of the same protein · chain A 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 O75581
Elsewhere: RCSB PDB 3S94 · PDBe 3S94 · UniProt O75581

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