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Monomeric darpin E2 complex with epor

Analyse Monomeric darpin E2 complex with epor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MOE
Type: protein
Length: 755 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E2 darpin; Erythropoietin receptor
UniProt: P19235
Ligands: PO4
Pockets: 7 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	E2 darpin	protein	161	55% helix, 0% strand	—
C	Erythropoietin receptor	protein	217	11% helix, 42% strand	P19235
D	Erythropoietin receptor	protein	216	9% helix, 45% strand	P19235

Ligands and binding sites

PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	573	0.71	0.79	65	PO4
2	560	0.71	0.80	68	PO4
3	326	0.58	0.77	39	empty
4	105	0.36	0.74	14	PO4
5	81	0.35	0.75	15	empty

Interfaces

5 interfaces between chains.

A–D · 868 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 860 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 732 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 239 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 152 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6MOE · Monomeric DARPin E2 complex with EpoR · the same entry in another collection · chain A against A, TM-score 1.00
P19235 · AlphaFold monomer V2.0 prediction for erythropoietin receptor (P19235) · a predicted model of the same protein · chain C against A, TM-score 0.95

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 P19235
Elsewhere: RCSB PDB 6MOE · PDBe 6MOE · UniProt P19235

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