Research workbench

Designed pentameric proton channel qlql

Analyse Designed pentameric proton channel qlql in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7UDX
Type: protein
Length: 372 residues
Chains: 15
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: De novo designed pentameric proton channel qlql
Pockets: 10 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 92% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, L, N	De novo designed pentameric proton channel qlql	protein	25	92% helix, 0% strand	—
K, M, O	De novo designed pentameric proton channel qlql	protein	24	92% helix, 0% strand	—

Ligands and binding sites

OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · chains C, D, N, O

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

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	473	0.84	0.90	37	empty
2	113	0.76	0.95	25	empty
3	131	0.70	0.90	27	empty
4	152	0.70	0.89	25	empty
5	260	0.65	0.81	29	OLC

Interfaces

38 interfaces between chains.

F–J · 660 Å² buried · 2 hydrogen bonds · protein-protein
H–I · 641 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 639 Å² buried · 3 hydrogen bonds · protein-protein
M–N · 631 Å² buried · 3 hydrogen bonds · protein-protein
A–B · 624 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

7UDX · Designed pentameric proton channel QLQL · the same entry in another collection · chain L against L, 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 7UDX · PDBe 7UDX

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