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K2P2.1 (trek-1):ML335 complex, 50 mm K+

Analyse K2P2.1 (trek-1):ML335 complex, 50 mm K+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W87
Type: protein
Length: 556 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Potassium channel subfamily K member 2
UniProt: P97438
Ligands: D12, R16, LNK, Q6F, D10, K, CD
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Potassium channel subfamily K member 2	protein	276	78% helix, 0% strand	P97438
B	Potassium channel subfamily K member 2	protein	280	74% helix, 0% strand	P97438

Ligands and binding sites

D12 · Dodecane · ligand · 4 copies · chains A, B
R16 · Hexadecane · ligand · 3 copies · chains A, B
LNK · Pentane · ligand · 3 copies · chains A, B
Q6F · N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl) amino]benzamide · ligand · 2 copies · chains A, B
D10 · Decane · ligand · chains A, B
K · Potassium ion · metal · 5 copies · chains A, B
CD · Cadmium ion · metal · 4 copies · chains A, B
UND · Undecane · additive · 3 copies · chains A, B
OCT · N-octane · additive · 2 copies · chains A, B

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	1197	0.76	0.78	113	Q6F, CD
2	585	0.66	0.76	42	K, LNK
3	240	0.63	0.81	33	empty
4	93	0.55	0.85	16	empty
5	166	0.50	0.77	25	empty

Interfaces

1 interface between chains.

A–B · 5203 Å² buried · 48 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6W87 · K2P2.1 (TREK-1):ML335 complex, 50 mM K+ · the same entry in another collection · chain A against A, TM-score 1.00
P97438 · AlphaFold monomer V2.0 prediction for potassium channel subfamily K member 2 (P97438) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 P97438
Elsewhere: RCSB PDB 6W87 · PDBe 6W87 · UniProt P97438

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