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Structure of MEMO1 C244S metal binding site mutant at 1.75A

Analyse Structure of MEMO1 C244S metal binding site mutant at 1.75A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7M8H
Type: protein
Length: 1,176 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein MEMO1
UniProt: Q9Y316
Ligands: GSH
Pockets: 14 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Protein MEMO1	protein	294	40% helix, 22% strand	Q9Y316

Ligands and binding sites

GSH · Glutathione · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 32 copies · chains A, B, C, D
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 3 copies · chains A, D
PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, D
GOL · Glycerol · additive · 3 copies · chains B, C, D

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

Pockets

14 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	1169	0.81	0.82	117	EDO
2	311	0.69	0.83	31	EDO
3	435	0.64	0.77	60	PEG
4	153	0.53	0.80	28	empty
5	135	0.47	0.78	21	EDO

Interfaces

5 interfaces between chains.

A–D · 557 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 493 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 467 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 459 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 440 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7M8H · Structure of Memo1 C244S metal binding site mutant at 1.75A · 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 A against A, TM-score 0.99

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 7M8H · PDBe 7M8H · UniProt Q9Y316

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