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Crystal structure of glycosylated human EPDR1

Analyse Crystal structure of glycosylated human EPDR1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6E8N
Type: protein
Length: 367 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mammalian ependymin-related protein 1
UniProt: Q9UM22
Pockets: 4 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mammalian ependymin-related protein 1	protein	185	5% helix, 49% strand	Q9UM22
B	Mammalian ependymin-related protein 1	protein	182	5% helix, 50% strand	Q9UM22

Ligands and binding sites

2PE · Nonaethylene glycol · additive · 2 copies · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.78	0.97	18	empty
2	860	0.77	0.80	70	2PE
3	774	0.77	0.81	65	2PE
4	85	0.72	0.95	20	empty

Interfaces

1 interface between chains.

A–B · 1828 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

6E8N · Crystal structure of glycosylated human EPDR1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9UM22 · AlphaFold monomer V2.0 prediction for mammalian ependymin-related protein 1 (Q9UM22) · a predicted model of the same protein · chain B against A, TM-score 0.97

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9UM22
Elsewhere: RCSB PDB 6E8N · PDBe 6E8N · UniProt Q9UM22

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