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K2P2.1 (trek-1):ML335 complex, 0 mm K+

Analyse K2P2.1 (trek-1):ML335 complex, 0 mm K+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W8F
Type: protein
Length: 557 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: R16, Q6F, 16C, LNK, D12, K, CD
Pockets: 13 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Potassium channel subfamily K member 2	protein	276	77% helix, 0% strand	P97438
B	Potassium channel subfamily K member 2	protein	281	74% helix, 0% strand	P97438

Ligands and binding sites

R16 · Hexadecane · ligand · 9 copies · chains A, B
Q6F · N-[(2,4-dichlorophenyl)methyl]-4-[(methylsulfonyl) amino]benzamide · ligand · 2 copies · chains A, B
16C · N-((E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl)palmitamide · ligand · chains A, B
LNK · Pentane · ligand · chains A
D12 · Dodecane · ligand · chains B
K · Potassium ion · metal · 4 copies · chains A, B
CD · Cadmium ion · metal · 4 copies · chains A, B

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

Pockets

13 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	1171	0.81	0.82	136	Q6F, CD
2	605	0.67	0.76	41	empty
3	84	0.53	0.85	17	empty
4	144	0.44	0.75	22	empty
5	132	0.44	0.76	21	empty

Interfaces

1 interface between chains.

A–B · 5175 Å² buried · 52 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6W8F · K2P2.1 (TREK-1):ML335 complex, 0 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 0.95

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 6W8F · PDBe 6W8F · UniProt P97438

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