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Structure of copper bound MEMO1

Analyse Structure of copper bound MEMO1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7L5C
Type: protein
Length: 1,170 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein MEMO1
UniProt: Q9Y316
Ligands: CU1
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Protein MEMO1	protein	293	40% helix, 23% strand	Q9Y316
B	Protein MEMO1	protein	292	40% helix, 23% strand	Q9Y316
D	Protein MEMO1	protein	292	40% helix, 22% strand	Q9Y316

Ligands and binding sites

CU1 · Copper (I) ion · metal · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 16 copies · chains A, C, B, D
GOL · Glycerol · additive · chains B

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

Pockets

9 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	1135	0.78	0.80	82	CU1
2	979	0.73	0.77	89	CU1, EDO
3	530	0.67	0.78	45	EDO
4	91	0.48	0.82	15	empty
5	119	0.46	0.79	17	empty

Interfaces

4 interfaces between chains.

A–C · 696 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 453 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 372 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 241 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

7L5C · Structure of copper bound MEMO1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y316 · AlphaFold monomer V2.0 prediction for protein MEMO1 (Q9Y316) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 Q9Y316
Elsewhere: RCSB PDB 7L5C · PDBe 7L5C · UniProt Q9Y316

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