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Crystal structure of deglycosylated human EPDR1

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

PDB: 6E7O
Type: protein
Length: 645 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mammalian ependymin-related protein 1
UniProt: Q9UM22
Pockets: 11 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 4% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Mammalian ependymin-related protein 1	protein	167	5% helix, 51% strand	Q9UM22
B	Mammalian ependymin-related protein 1	protein	161	4% helix, 54% strand	Q9UM22
C	Mammalian ependymin-related protein 1	protein	154	2% helix, 51% strand	Q9UM22
D	Mammalian ependymin-related protein 1	protein	163	5% helix, 51% strand	Q9UM22

Pockets

11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.78	0.98	20	empty
2	826	0.78	0.81	84	empty
3	96	0.78	0.98	21	empty
4	92	0.74	0.96	20	empty
5	375	0.66	0.79	31	empty

Interfaces

4 interfaces between chains.

A–B · 1648 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 1396 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 165 Å² buried · 1 hydrogen bond · protein-protein
B–C · 49 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

6E7O · Crystal structure of deglycosylated human EPDR1 · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.98

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 Q9UM22
Elsewhere: RCSB PDB 6E7O · PDBe 6E7O · UniProt Q9UM22

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