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De novo design of membrane protein--mini-evgl membrane protein, C2221 form-2

Analyse De novo design of membrane protein--mini-evgl membrane protein, C2221 form-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MQ2
Type: protein
Length: 126 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Mini-evgl membrane protein
Ligands: NH2
Pockets: 2 · best druggability 0.73

Structure

x-ray diffraction · 2 distinct chains · 90% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, E	Mini-evgl membrane protein	protein	25	92% helix, 0% strand	—
D	Mini-evgl membrane protein	protein	26	88% helix, 0% strand	—

Ligands and binding sites

NH2 · Amino group · ion · chains D
C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 5 copies · chains A, E, B, C, D

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	120	0.73	0.91	25	C8E
2	64	0.57	0.87	15	C8E

Interfaces

5 interfaces between chains.

C–D · 602 Å² buried · 0 hydrogen bonds · protein-protein
A–B · 586 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 577 Å² buried · 0 hydrogen bonds · protein-protein
A–E · 577 Å² buried · 0 hydrogen bonds · protein-protein
D–E · 575 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6MQ2 · De Novo Design of membrane protein--mini-eVgL membrane protein, C2221 form-2 · the same entry in another collection · chain A 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
Elsewhere: RCSB PDB 6MQ2 · PDBe 6MQ2

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